(Updates with Southwest response in third paragraph.)

July 28 (Bloomberg) -- Southwest Airlines Co. may have to pay one of the largest fines in Federal Aviation Administration history for continuing to fly some airplanes after being told that repairs to the aircraft didn’t live up to U.S. regulations.

The FAA is proposing a $12 million civil penalty against Southwest, which carries the most passengers in the U.S., for operating “numerous flights” in 2009 with inadequate repairs to the fuselage skins. The maintenance in question was designed to eliminate potential cracks on 44 of the airline’s Boeing Co. 737s, according to a statement today by the FAA.

The fine would be the second major civil penalty against the Dallas-based airline for maintenance lapses since 2008. The issues raised by the FAA were resolved and don’t relate to any aircraft currently used, Southwest said in an e-mailed statement.

“Southwest is committed to continuously making enhancements to our internal procedures, as well as improvements related to oversight of our repair vendors,” it said.

The repairs to the aluminum skin of the planes were done by a Southwest contractor, Everett, Washington-based Aviation Technical Services Inc., according to the FAA. Under U.S. law, airlines are responsible for repairs made by other companies.

Southwest has 30 days to respond to the proposed fine. The FAA often lowers penalties after negotiating with airlines.

Previous Fine

Southwest in 2009 agreed to pay $7.5 million in a case where the airline had made almost 60,000 flights on 46 of its fleet of Boeing 737s without making repairs mandated by the aviation regulator. The FAA had originally proposed in 2008 fining the company a then-record $10.2 million.

Since then, the FAA has proposed a $13.2 million penalty against Boeing in 2012 for delays in making fuel-tank safety equipment available, and the agency sought $24.2 million against the former American Airlines Inc. for improper repairs.

In the latest Southwest case, workers at Aviation Technical Services starting in 2006 applied the aircraft skin repairs in an unapproved way that may have allowed moisture to penetrate the skin, leading to corrosion. Workers also didn’t apply fasteners in all the required rivet holes, according to the release.

During the work, ATS failed to properly support the planes, which may compromise the repair work, FAA said.

The company didn’t immediately respond to a telephone message seeking comment.

The agency also found other violations, including a failure to properly attach wires on two planes to protect against lightning strikes.

The airline flew each of those planes on more than 20 passenger flights after Southwest realized it was in violation, the FAA said.

“The FAA views maintenance very seriously, and it will not hesitate to take action against companies that fail to follow regulations,” FAA Administrator Michael Huerta said in the statement.

To contact the reporters on this story: Alan Levin in Washington at alevin24@bloomberg.net; Michael Sasso in Atlanta at msasso9@bloomberg.net To contact the editors responsible for this story: Romaine Bostick at rbostick@bloomberg.net Elizabeth Wasserman