Which parts fail
Components named in complaints (automatic and manual transmissions, CVT, axles, driveshaft, 4WD/AWD).
Mileage when the problem started
Owner reports
Selected complaints filed with NHTSA by 1999 Mercury Cougar owners, lightly cleaned up (personal details are redacted by NHTSA).
The battery seemed low on the car, indicated by interior lights not being very illuminated, but then dashboard lights started flashing and windows rolled up very slowly. I charged the battery for many hours and it took a charge, so I could get to the Mercury dealer. It died when I got there and they were closed, so I had to jump it and move to a safe location to leave overnight. This had happened twice before in the past 2 1/2 years, so I new it was the alternator again! That's three alternators in 2 1/2 years. This time I am out of warranty and am expected to pay $550 for a recurring problem that clearly will happen again. The dealer can not tell me why this is occuring, and Ford "customer service" could care less. After researching this problem on the internet, it seems that many Cougar owners have experienced this problem continually. …
While the car is running, my 1999 Mercury Cougar will shift from drive to neutral, to reverse, without ever releasing the lock. All it takes is slight pressure on the gear shift to change gears unintentionally. The dealer I just bought the car from 2 weeks ago, and Ford tell me that it is normal for the gears to move from drive to neutral with no effort. The dealer said no harm is done. You are just driving down the road at 60 miles an hour when you bump the gear shift, and lose all acceleration until you move the gear shift back to drive. I can see a real safety issue there. And, considering that this is my 16 year old's car, I see a real safety issue. It also would shift from 2nd all the way to neutral without releasing the lock.
I was driving down an interstate road on the morning of July 3rd 2000. A considerable amount of rain had fallen on the road and it was still raining slightly the section of the road that I was on was completely straight. I was in the left lane doing about 55mph on the 65mph road when I felt the car lurch and begin to turn toward the left. I looked down at my instrument panel and noticed that my tachometer was on zero and my warning lights were all on. The car started to spin counterclockwise very quickly and crossed over three lanes of traffic where it finally crashed into a guardrail on the right side of the road. I was facing oncoming traffic when the car finally settled.
The car was driving fine. I got in it, started it, and put it in reverse, and it didn't go. I put it back in park, then in drive, and I couldn't go forward because of the curb. So I put it in reverse again, eventually, I was able to pull back out of my parking spot, but it went back hard, and I could have hit another car if one was in the space behind me, and when I did, it was very stuttered movement. When I p went forward (drive), it had a rubbing sound, like something was rubbing on something. We haven't done anything to this car because we have no money to even tow it. I just bought this car 5 months ago. It has run very well until this day.
Purchased car new, in 57000 miles we have had to replace, 2 alternators, 1 starter, 2 batteries, entire rack and pinion, power steering pump, transmission torque converter, 4 set of brakes, 4 sets of tires plus two individual tires all with sidewall blow outs except one puncture and 2 headlight switches, 2 cig lighters. The entire upper engine gasket set had to be replaced to get to an intake leak. The head lights and foglights work itermittantly, engine warning lights are constantly going on and off. Currently one headlight is out (lamp is good) fog lights are not working (today) and an engine warning light is indicating a problem again.
I own a 1999 Mercury Cougar which currently has 5700 miles. The flywheel has failed ,resulting in complete replacement of the starter and flywheel. The problem began more than a year ago but was so intermittent that my mechanic could not reproduce the problem in order to diagnose. At this time the vehicle is being repaired. Damaged parts will be retained for future inspection if needed. I conducted a websearch and found a website which contained many other owners of 99 cougars experiencing the exact same problem, even at the same approx. Mileage. The website is located at: ://www.carsurvey.org/viewcomments_review_5988.html.
I own a 1999 Mercury Cougar. I have maintained the vehicle per the service manual through the local Mercury dealership. Sometime during early April 2005, I noticed that the car hesitated and jerked violently after about fifteen minutes of normal driving. We were able to drive the car in for service. The dealer "diagnosed" the problem and replaced a part. The car continued to malfunction the very next day. I returned to the dealership and was told that the problem was with transmission. I have had the transmission replaced by a local Ford dealership. I am not sure whether the old transmission is available.
Dt*: the contact stated the exterior brake lights did not illuminate at all, causing the vehicle to nearly get rear-ended while braking from traveling 70 MPH. The vehicle was taken to a private repair shop, who determined that the wiring harness needed replacement due to a short circuit. There was a NHTSA recall #01V032000 pertaining to the brake light switch. The vehicle was not included in the recall due to the VIN. Secondly, the engine hesitated while warming up, accompanied by a rough idle. The vehicle was not seen by a mechanic.
Loud grinding noise from the manual transmission occurs when car is down shifted to first gear coming to a stop, or shifted to first not being at a complete stop, the shift lever "pops out of gear" and admitting a very loud grinding noise. Preventing this would be coming to a complete stop from neutral, then after stopping completely proceed to engage clutch and put car into first gear. First gear sometimes hard to shift into, might be a shift linkage problem. Sounds like the manual transmission grinding with a loud winding squeal.
The transmission axle light is on and the dashboard says odometr off then the transmission axle light comes on and the car shifts hard. This happened at 49,000 miles the dealer said I would need a new transmission. I replaced transmission, and now at 75,000 miles the same thing is happening. This seems to be like there is some defective problem going on. I was very upset that the warranty didn't cover this as it happened over 36,000 miles but I refuse to have to again pay thousands of dollars for another transmission.
Transmission complaints in other Cougar years
Frequently asked questions
How common are transmission problems on the 1999 Mercury Cougar?
NHTSA has 50 complaints about the transmission & drivetrain of the 1999 Mercury Cougar, 11% of the model year's 454 complaints. The component named most often is automatic transmission (31 mentions).
Is there a recall for 1999 Mercury Cougar transmission problems?
No. NHTSA lists no transmission & drivetrain recall for the 1999 Mercury Cougar, though it has 7 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 1999 Mercury Cougar transmission problems start?
Half of the complaints with a recorded mileage happened before about 77,000 miles, and 9% before 25,000 miles.
Is it dangerous?
Owners linked 1 crash, 0 fires and 1 injury to transmission & drivetrain 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.