Which parts fail
Components named in complaints (engine, cooling system, oil leaks, timing chain, exhaust).
Mileage when the problem started
Owner reports
Selected complaints filed with NHTSA by 2006 Lincoln Navigator owners, lightly cleaned up (personal details are redacted by NHTSA).
I was driving at about 40 MPH on a two lane road and my Navigator just shut off. I looked at the instruments and it said engine fail safe mode. I pulled over as best I could and placed the vehicle in park and turned it back on. Luckily I was only about 3 minutes away from home. I read the manual and it mentioned coolant. I checked the coolant but it is completely full. I've been reading about this issue and it seems as if there's a flaw. I've read about how people take their cars in and have different diagnosis and the issue does not get fixed. I will be taking my vehicle in to Ford but I'm worried that I'm going to be charged a lot of money and it May not even repair the issue. There are many complaints about the engine fail safe mode with vehicles shutting off on the highway. I'm afraid to drive my car even after I take it in to Ford. …
Tl* the contact owns a 2006 Lincoln Navigator. The contact stated that while stopped at a stop sign and attempting to move forward, the accelerator pedal was depressed however, the vehicle hesitated. The check engine warning light then illuminated. The contact also stated that while attempting to park the vehicle on another occasion the vehicle stalled. Additionally, on another occasion while driving at approximately 30 MPH, the accelerator was depressed however, the vehicle failed to respond. The vehicle was taken to an independent mechanic to be diagnosed. The contact was informed that the spark plugs and catalytic converter needed to be replaced. (north park Lincoln located at 9207 san pedro avenue, san antonio, tx 78216) was contacted and informed of the failure. The vehicle was not repaired. The manufacturer was not informed of the failure. …
Tl* the contact owns a 2006 Lincoln Navigator. While driving at 35 MPH, the vehicle stalled without warning. The contact was able to restart the vehicle after several attempts. The contact stated that the issue recurred several times. The vehicle was taken to a dealer where it was diagnosed that the alternator failed. The alternator was replaced, but the failure persisted. The vehicle was brought to the dealer a second time and the alternator was again replaced. The contact stated the issue still persisted. The vehicle was taken to an independent mechanic but the vehicle was not diagnosed. The vehicle was not repaired. The failure mileage was 48,000.
Tl 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 sustained injuries to her face. The current and failure mileages were 32,000.
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 happened again September 23, 2010 after it was supposed to have been fixed by changing a sensor. This is extremely dangerous!! Car shuts down and my wife was almost rear ended at highway speeds. On google search of "Lincoln Navigator fail safe mode problems" there are 1380 results. Goes to over 2500 when 2006 is removed. During first "fix" Ford dealership replaced a sensor but the details are not documented in my file on the Ford/Lincoln computer system. …
2006 Lincoln Navigator, 50,000 miles on car. Car shut down after giving an engine safety mode error on dash while on four lane busy highway traveling 40-45 MPH. Coasted to side of road (no berm available). Cars racing by. Waited 5 minutes. Restarted car and limped into team Ford of marietta georgia dealer. I was told the throttle control body & motor asy #8l3z*9e926*a was bad and was not covered under the $1,000 extended warranty I purchased on the car in 2006. Repair bill was $800 out of pocket. Checked online and this is a known issue for Ford expeditions & Lincoln Navigator engines and yet Ford does nothing to fix. Does someone have to die to get Ford to repair these defective parts? Nothing more dangerous than a car that shuts down in heavy traffic traveling at high speeds.
2006 Lincoln Navigator, 60,000 miles on car. Car shut down after giving an engine failed safety mode error on dash while on four lane busy highway traveling 40-45 MPH. Coasted to side of road (no berm available). .. Waited 5 minutes. Restarted car and limped into gary yeoman Ford dealer. I was told the throttle control body & motor asy #3l3z*9e926*a was bad and was not covered under the extended warranty I purchased on the car in 2009. Repair bill was $900 out of pocket. Checked online and this is a known issue for Ford expeditions & Lincoln Navigator engines and yet Ford does nothing to fix. Does someone have to die to get Ford to repair these defective parts? Nothing more dangerous than a car that shuts down in heavy traffic traveling at high speeds.
Tl contact owns a 2006 Lincoln Navigator. During routine maintenance and a tune-up, he received a call from the mechanic stating that they broke part of the spark plug into the engine cylinder while trying to change them. The dealer would not assume liability for the repair. The necessary repairs were performed on the vehicle at the owner's expense. On a separate occasion, while driving at speeds of less than 35 MPH the vehicle stalled without warning. The vehicle was towed to the dealer where they found the fuel pump computer module failed. The vehicle was repaired at the owner's expense. The failure mileage was 96,000 and the current mileage was 100,000. Updated 11/22/10 updated 11/23/10
1: 10/19/08 I was driving 70+MPH and all of sudden car gives an engine failure/safe mode signal which locked wheel, not allowing acceleration. Once able to get to side of the road, I had to try at least 2 times until finally car turned on. It was towed and dealership could not find any problems. 2: 11/16/07 started car drove about 2-3 miles and then when I had to restart the car, it did not come on. It was towed and battery was replaced 3: 7/16/08 turned on car, drove for almost 2miles, stopped at a light and when I had to accelerate, the car gave me a engine failure/safe mode signal. Dealership could not find anything wrong with it.
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 vehicle was being driven around 45 MPH on 4 lane highways/roads. We had a 2003 expedition that had the same problem. Ford motor company definitely has a design issue that impacts safety and they do not want it known.
Engine complaints in other Navigator years
Frequently asked questions
How common are engine problems on the 2006 Lincoln Navigator?
NHTSA has 22 complaints about the engine & cooling of the 2006 Lincoln Navigator, 37% of the model year's 60 complaints. The component named most often is engine (5 mentions).
Is there a recall for 2006 Lincoln Navigator engine problems?
No. NHTSA lists no engine & cooling recall for the 2006 Lincoln Navigator, though it has 3 recalls for other components. If the problem is widespread, a repair may still be covered by an extended warranty or a manufacturer service bulletin — ask a dealer.
At what mileage do 2006 Lincoln Navigator engine problems start?
Half of the complaints with a recorded mileage happened before about 68,000 miles, and 5% before 25,000 miles.
Is it dangerous?
Owners linked 1 crash, 1 fire and 1 injury to engine & cooling problems on this model year. If you notice symptoms, have the car checked before driving further.
Source: U.S. National Highway Traffic Safety Administration (NHTSA) — owner complaints through October 20, 2026, recalls and defect investigations; fuel economy from the EPA. Complaints are unverified reports and are not proof of a defect. How we rate model years.