The Federal Aviation Administration said Monday that it planned to fine Southwest Airlines $12 million for repair violations on some of its Boeing 737 jets, citing faulty repairs it said the airline had made since 2006.

Southwest has 30 days to respond to the FAA’s complaint and can negotiate to reduce the fine.

In one long-standing case, the FAA alleges that Southwest conducted “extreme makeover” alterations to eliminate cracking on the aluminum skin of 44 of its jets.

The agency said it found that a contractor, Aviation Technical Service, based in Everett, had not followed the proper repair procedures for replacing fuselage skins.

The airline responded Monday that the complaint included repairs that were fully resolved some years ago and did not affect airplanes currently in operation, according to a statement by Brandy King, an airline spokeswoman.

“We always strive for full compliance with established and approved processes and procedures,” the statement said.

The FAA contends that contractors working under the airline’s supervision had failed to install fasteners in all of the rivet holes after they had applied sealant under new skin panels.

As a result, the FAA said, this “could have resulted in gaps between the skin and the surface to which it was being mounted. Such gaps could allow moisture to penetrate the skin and lead to corrosion.”

The fine stems from a period in 2009 when the airline flew those planes even after the agency put Southwest on notice that the planes were not in compliance with approved repair methods. The agency, however, said it had “later approved the repairs after the airline provided proper documentation that the repairs met safety standards.”

The FAA also claims that workers did not properly place the airplanes on jacks and shore them up while the work was being done. If a plane is shored improperly during skin replacement, the airframe could shift and lead to problems with the new skin, according to the FAA.

In a separate case, the FAA also said it found that Southwest failed to properly install a ground wire on water drain masts on two Boeing 737s in response to a federal directive addressing lightning strikes on those components. The airline operated each of those airplanes on more than 20 flights before correcting the problem.

The largest penalty imposed by the FAA on an airline was against American Airlines and three of its subsidiaries, which agreed in May 2013 to pay $24.9 million in fines related to the forced grounding of the airline’s MD-80 fleet in 2008 after inspections found that some wiring modifications had been improperly done. The FAA initially had sought $162 million from the companies.