Various vehicles equipped with a 4.6L, 5.4L, 6.8L modular 3 valve engine built on or before 8-Jan-2016 may exhibit symptoms that may include upper end engine noise, rough running, misfire and/or engine damage. If diagnosis leads to only camshaft/camshaft roller follower(s) requiring replacement, replace all of the camshaft roller followers on both banks/cylinder heads with part number 3L3Z-6564-A, not just the faulty roller follower(s). When replacing the camshaft roller followers, refer to Workshop Manual (WSM), Section 303-01.
full bulletin at NHTSA ↗2006 Lincoln Navigator engine problems
severe 18 complaints filed with NHTSA · avg repair $3,100 · see engine across all vehicles →
Failure mileage
Complaints
18
Recalls
0
Avg fix
$3,100
1crash
1fire
1injury
When does it fail?
Of the 18 engine complaints filed for the 2006 Lincoln Navigator, here's the actual mileage breakdown — failures cluster heaviest at 25,000-50,000 mi.
0-25k
25-50k
50-75k
75-100k
100-125k
125-150k
150k+
Each bar shows the share of total complaints filed at that mileage range. Peak failure window highlighted. Some owners report problems earlier; some make it well past 150,000 miles symptom-free. Maintenance habits and driving conditions shift the curve as much as mileage alone.
What stands out
Of the 9 model years of Lincoln Navigator we track for engine problems, this one carries the most owner complaints on file — 18.
Engine accounts for 30% of every owner complaint on file for this vehicle — the dominant problem area across 5 categories tracked.
Is there a fix? Manufacturer service bulletins
The manufacturer has issued service bulletins covering engine on this vehicle — documented repair instructions, service campaigns, or warranty extensions sent to dealers. A TSB isn't a recall (it's not a free safety remedy), but it's the manufacturer acknowledging the issue and how to fix it.
The Powertrain Control/Emissions Diagnosis (PC/ED) manual has been revised for diagnosing electronic throttle bodies (ETBs). The ETC_ACT and ETC_DSD PIDs should not used to diagnose possible ETB concerns. The IDS has a limited refresh rate when reading these PIDs and cannot display quickly enough to validate a concern. The PCM automatically monitors these inputs more accurately and will set diagnostic trouble codes (DTCs) when appropriate. Using these PIDs for diagnostics will lead to inaccurate results and improper ETB replacements. If a concern is intermittent and no DTCs are present, refer to historical DTCs and the PC/ED, Section 3 No DTCs Present Index chart for further information.
full bulletin at NHTSA ↗LINCOLN/FORD: WHEN DRIVING FROM IDLE UP TO 1200 RPM, THERE MAY BE AN INTERMITTENT RATTLE NOISE COMING FROM ENGINE. 2004-2013 F-150, F-250, F-350, EXPEDITION, MARK LT, NAVIGATOR.
full bulletin at NHTSA ↗FORD/LINCOLN/MERCURY: MAY HAVE SLUDGE BUILDUP IN THROTTLE BODY LEADING TO LESS AIRFLOW OR ENGINE IDLING RPM FLUCTUATION AND HARD STARTS OR BATTERY DISCONNECT OR DEAD BATTERY AFTER KEEP ALIVE MEMORY (KAM) CLEAR. MODELS 2003-05 THUNDERBIRD, 05-06 MUSTANG, 06-08 FUSION, 04-05 EXPLORER, 05-06 EXPEDITION, 05-07 F-150; 2003-06 LS, 06 ZEPHYR, 05-06 NAVIGATOR; 06-08 MILAN.
full bulletin at NHTSA ↗WDS COP KIT DIAGNOSTIC TIP - COIL ON PLUG (COP) IGNITION SYSTEMS - ENGINE MISFIRE OR ROUGH RUNNING.
full bulletin at NHTSA ↗Source: NHTSA manufacturer communications. Bring the bulletin number to your dealer or shop.
The failure pattern owners describe
The 2006 Lincoln Navigator has two major engine problems that overlap across these complaints. First, engine fail-safe mode shutdowns occur at highway speeds with little warning—the warning light comes on, the engine dies, and the vehicle coasts to a stop. Owners report this has happened repeatedly, sometimes ten or more times. The vehicle usually restarts within minutes, but the hazard is real: drivers at 40–70 mph on busy highways nearly get rear-ended. Dealers have replaced throttle control bodies ($800–$900), reprogrammed computers, and swapped fuel pumps, yet the problem persists even after multiple visits. One owner's friend in a different state has the same truck with identical failures.
Second, spark plugs are breaking inside the cylinder head—either during routine service or on their own. When this happens, the plug debris damages the head, and repairs balloon to over $3,000 for a new head or complete engine. Dealers have refused to cover these failures under warranty, claiming customer liability even when the dealer technician broke the plugs during service.
One complaint describes a fire and crash at 32,000 miles with undetermined cause. Owners consistently note that Ford is aware of these issues but has issued no recalls or fixes. The fail-safe shutdowns are particularly dangerous because they can happen anywhere and dealers frequently cannot isolate why.
Failure modes owners describe
Engine fail-safe mode shutdown
Vehicle enters fail-safe mode and shuts down while driving, typically triggered by throttle control body failures or unidentified sensor/computer issues. Engine usually restarts after shutdown.
When: Occurs at various mileages (50k–140k miles) and speeds (25–70+ mph); no clear pattern but frequently during acceleration or highway driving.
Symptoms owners cite: Engine fail-safe mode warning light illuminates; Vehicle loses power and stalls immediately; Loss of power steering reported in at least one instance; Engine restart successful after several seconds to minutes
Repairs/costs cited: Throttle control body and motor assembly replaced ($800–$900 at dealers); fuel pump replaced in at least one case; ECU/computerized system reprogrammed; multiple dealer visits often unsuccessful in isolating root cause.
Recalls/TSBs owners mention: Manufacturer contacted in several cases with no resolution offered; no recalls mentioned; extended warranties did not cover throttle control body failures.
Spark plug failures and breakage
Spark plugs fail prematurely, break during service, or eject from cylinder head. Broken plugs can damage cylinder head, requiring head replacement or engine overhaul.
When: Occurs during routine spark plug changes and at various mileages (44k–100k miles); also happens spontaneously without service.
Symptoms owners cite: Engine missing/hesitation during acceleration; Check engine light illumination; Spark plug breaks off inside cylinder during service; Spark plug ejects from engine; Vehicle stalls at idle RPM after spark plug replacement; Hard starting or rough idle
Repairs/costs cited: Spark plugs replaced; cylinder head repair/replacement required when plugs break inside engine (costs exceed $3,000 in one case); one owner reported dealer broke 5 of 8 spark plugs and refused warranty coverage; another dealer broke spark plug during service and owner paid for repair.
Recalls/TSBs owners mention: Owners cite this as a known Ford design flaw; dealers refused liability in spark plug breakage cases; no manufacturer-initiated recalls or technical service bulletins mentioned.
Fuel pump and computer module failure
Fuel pump computer module fails, causing engine stall without warning. Vehicle must be towed for repair.
When: Around 96,000 miles in documented case.
Symptoms owners cite: Vehicle stalls without warning while driving at low speed; No warning lights before stall
Repairs/costs cited: Fuel pump computer module replacement required; repair performed at owner's expense.
Engine fire and crash
Vehicle crashed into another vehicle at 50 mph, then caught fire with multiple explosions under the hood.
When: At 32,000 miles.
Symptoms owners cite: Flames visible under hood immediately after collision; Vehicle exploded five times; Fire department required to extinguish
Repairs/costs cited: Vehicle totaled; fire cause listed as undetermined.
Recalls/TSBs owners mention: None documented; police report filed.
Engine misfiring and head damage
Engine misfires persistently after coil replacement; investigation reveals burnt cylinder head, with possibility of deeper engine damage. Head repair unsuccessful; engine replacement suggested.
When: At 44,000 miles.
Symptoms owners cite: Persistent misfiring after ignition coil replacement; Engine runs rough
Repairs/costs cited: Ignition coils replaced; cylinder head sent for outside repair; new engine replacement being considered by dealer; warranty coverage uncertain.
Synthesized from 18 NHTSA owner complaints — unverified consumer allegations, summarized for patterns. The verbatim filings appear below.
What owners are reporting 6 most recent
The Lincoln dealership broke 5 of my 8 spark plugs while trying to change them. I was told that I have to pay since this has happened. This is a known problem with Ford engines. Please reference the following link. Http://www.fordproblems.com/spark-plug-ejected-from-engine.shtml. *tr
2006 Lincoln navigator, with just over 100,000 miles on vehicle. Vehicle shut down immediately after giving an engine failed safety mode error on dash. Fortunately my wife was driving in the neighborhood and doing 25 MPH. Muscled it over to the side of the road and restarted the vehicle. This is about the 4th time this has happened in the 5 years we have owned the vehicle. The other times the…
Tl*the contact owns a 2006 Lincoln navigator. While driving 50 MPH, the vehicle crashed into the rear of another vehicle. The air bags deployed and flames were noticed under the hood. The vehicle exploded five times. The fire department extinguished the fire and the vehicle was towed. A police report was filed. The cause of the fire was undetermined. The driver of the other vehicle…
2006 navigator would keep misfiring even after coils were replaced. Dealer first reports it was a valve. After inspection valve was not the problem but a burnt head was the cause. Head went to outside shop for repair but the shop says now that the problem might be lower in the engine. A new engine is being suggested by the dealer but the warranty company may not pay. Car has 44000 miles…
2006 Lincoln navigator. Fail safe mode comes on while driving and shuts vehicle down. This has happened twice and also exact same incident to friend in different state with same 2006 navigator. Decided to report after I called Lincoln and they had record of my call in december 2009 and january 2010 but no record of the work performed to correct the problem or the dangerous incident. It…
Was driving on the highway and the vehicle went into engine failsafe mode. Was able 2 pull over and turn engine off and restart with no prob. This has happened at least 10 more times since always on acceleration luckily I was not in accidents. Most of the shut offs have been in highway driving conditions at speeds over 55 MPH. After research seems this is hard 2 diagnose but Ford is aware of…
Had engine trouble with your 2006 Lincoln Navigator?
File a complaint with NHTSA → It's free, official, and how every report above got here — owner filings are the federal safety record this page is built on.
Common questions
How serious is the engine problem on the 2006 Lincoln Navigator?
It's a meaningful issue. 18 complaints have been filed and the failure mode causes operational problems for owners. Repairs average $3,100.
At what mileage does the engine typically fail?
Across the 15 complaints that reported odometer mileage, most engine failures cluster between 44,102 and 101,320 miles, with the median around 74,000. A quarter of owners report trouble before 44,102; a quarter make it past 101,320. Maintenance history matters more than the odometer alone — this is the reported failure window, not a guarantee.
What does it cost to fix?
Independent shops typically charge around $3,100 for engine repairs on this vehicle. Dealer pricing tends to run 20-40% higher. The exact figure depends on the specific failure mode, parts availability, and your local labor rates. If you're outside factory warranty, an extended service contract often covers this category.
Are there any recalls related to engine?
No active recalls currently cover engine issues on this vehicle. The complaints filed represent owner-reported failures that haven't risen to the level of a manufacturer-issued recall — but they're still worth knowing about before you buy or budget for repairs.
Related
Complaint and recall data sourced from the National Highway Traffic Safety Administration (NHTSA)
public records database. Verify the raw federal record at
nhtsa.gov/vehicle/2006/Lincoln/Navigator.
Severity ratings are derived from reported crashes, fires, injuries, and fatalities. Repair cost estimates are
independent-shop national averages and may differ in your area. Some links on this page are affiliate links.