American Airlines has joined forces with British Airways
US aviation officials have accused American Airlines of major breaches of safety, including intentionally flying planes known to need repairing.
The Federal Aviation Administration (FAA) said it wanted to fine the company a total of $7.1m (£3.8m).
It said two MD-83 passenger jets were used on dozens of flights in 2007, even though repair work reported as necessary by pilots had not been done.
Problems with drug and alcohol testing were also found, officials said.
American Airlines, which can appeal against the fine, had no immediate comment.
The FAA statement comes hours after British Airways confirmed it had sealed an alliance with American Airlines, allowing the two carriers to agree fares, routes and schedules together.
The alliance also includes Spain's Iberia, which is merging with BA.
In a statement, the FAA said that in December 2007, "American used the wrong provisions of its Minimum Equipment List (MEL) to return two MD-83 aircraft to service after pilots had reported problems, and flew the planes 58 times in violation of FAA regulations".
The MEL contains components and systems without which the aircraft may operate safely under specific limitations.
On 11 and 12 December, the airline "operated the first MD-83 on eight flights in airspace it should have been restricted from after maintenance on part of the autopilot system was improperly deferred", the FAA said.
An FAA inspector discovered the error and informed American Airlines, but the plane was still flown on 10 further flights until the problem was fixed, it added.
In another incident involving the same aircraft on 21 December, the autopilot disconnected during landing because of a faulty altimeter.
However, technicians did not check the problem and instead deferred maintenance, allowing a further 36 flights to take place, the FAA said.
A second MD-83 also experienced an "autopilot disconnect" on 27 December.
"Although American mechanics correctly diagnosed the problem, they again deferred maintenance under the wrong item of the MEL. As a result, the aircraft operated on four revenue flights without a fully functioning autopilot," the FAA said.
The FAA proposed a $4.1m civil penalty for the violations in the first case and $325,000 for the second. It said the fines were appropriate because the airline deferred repairs even when it was aware.
"In intentionally continuing to fly the aircraft, the carrier did not follow important safety regulations intended to protect passengers and crew," the FAA said.
The FAA is also proposed $2.7m in civil penalties for "alleged past deficiencies in its drug and alcohol testing programs and for allegedly operating aircraft in past years without timely inspections of emergency escape path lighting systems".