The Federal Aviation Administration is seeking civil penalties from Continental Airlines for violating three safety regulations, after a month-long investigation of its operations and maintenance practices, FAA officials said.

The alleged violations are all that is left on a list of 52 possible discrepancies FAA inspectors developed when they gave the airline a thorough going-over in February and March, after the Air Line Pilots Association (ALPA) charged that Continental was operating unsafely.

ALPA has been on strike against Continental since September 1983, shortly after the airline declared bankruptcy, ceased domestic operations, abrogated its labor contracts, and resumed operations three days later with new wage scales and work rules that cut pilots' pay by more than half.

The FAA report, dated April 20, was obtained this week by The Washington Post under the Freedom of Information Act.

Continental is "providing an adequate level of safety in their flight operations and aircraft maintenance programs," the report said. "However, system deficiencies and discrepancies were noted in several key program areas," including training, quality control in maintenance and the check-airman program, it said.

Check airmen are company pilots deputized by the FAA to qualify other company pilots. The FAA now agrees that Continental's check-airman program followed agreements worked out by the airline and FAA inspectors, even if there were technical violations. The program has been changed.

H.C. McClure, chief of the FAA's Western Pacific Region, which holds Continental's license to operate, said in an interview that "There are no serious findings in that report. . . . There are a number of findings that are paperwork findings, things you would expect if you went in to any carrier."

Outstanding are alleged violations of regulations requiring the training of crews in the handling of hazardous materials and a flight by a Continental pilot one day after his proficiency check had expired, the aeronautical equivalent of driving with an expired license.

Continental can be fined a maximum of $1,000 for each violation; it is unknown how many violations the FAA is alleging under the hazardous-materials issue. The FAA will seek a penalty against the pilot for flying without a current check and against the airline for permitting it, McClure said.

Nine of the 52 alleged discrepancies were closed administratively with letters of correction, and the others were dismissed with no action after discussions with Continental officials, McClure said.

Many discrepancies stemmed from Continental's merger with Texas International in October 1982. The better-known Continental name was used after the merger. Continental is a subsidiary of Texas Air Corp., which also owns New York Air.

Inspectors found that Continental tracked airworthiness directives for its Boeing 727s and McDonnell Douglas DC10s one way, while Texas International tracked them another for its McDonnell Douglas DC9s. An airworthiness directive is a safety-related maintenance requirement carrying the force of law. The procedures have now been integrated. Other differences have been resolved in training programs and manuals for flight attendants.

Continental has improved weather information for some of its pilots after discussions with the FAA, documents from both parties show.

Clark Onstad, vice president for government affairs at Continental, said yesterday that "when you do a merger, there is a natural tension between labor contracts of the merged carriers and the ability to bring about greater operational efficiency." Those tensions contributed to the problems of integrating operations and training, he said.