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

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

In one longstanding case, the F.A.A. 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, Wash., had not followed the proper repair procedures for replacing fuselage skins.

The airline responded on 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 F.A.A. contends that contractors 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. This “could have resulted in gaps between the skin and the surface to which it was being mounted, the F.A.A. said. “Such gaps could allow moisture to penetrate the skin and lead to corrosion,” it added.