Southwest Airlines
A Southwest Airlines jet waits on the tarmac at Denver International Airport in Denver on Jan. 22, 2014. Reuters/Rick Wilking

The U.S. government has sued Dallas-based Southwest Airlines Co. after a settlement could not be reached over the airline's move of hiring a contractor to make extensive repairs on some of its planes that failed to meet federal safety standards. The U.S. Department of Justice, or DOJ, is seeking civil penalties worth $12 million against the company.

The justice department filed the case in a federal district court in Washington state and the penalty will be the second-largest amount sought against an airline by the FAA, after a $24.2 million claim made against American Airlines. The government claimed that, in 2006, Southwest hired Everett, Washington-based Aviation Technical Services Inc. to reinforce the aluminum skins of 44 planes to keep them from cracking. But, according to the government, the contractor did not follow the right procedures, Associated Press, or AP, reported.

"We dispute the FAA's allegations and look forward to the opportunity to vigorously defend Southwest's record in a court of law," Brandy King, a spokesperson for the airline, said, according to AP, on Monday night.

One of the most serious components of the current case is the replacement of parts on the planes’ fuselages. According to the FAA, Aviation Technical Services put sealants under the new skin panels of Southwest's planes but did not install all the rivets fast enough to make the sealant effective. The misstep could cause corrosion as the gaps could allow moisture to penetrate the skin, the FAA claimed.

Although the company returned most of the planes for further repairs in 2009, it kept flying some of its jets until the FAA warned the company, according to AP. The later repairs were approved by the regulators, the report said.

In 2008, the FAA had sought a penalty of $10.2 million from Southwest Airlines for improper maintenance of its aircraft, but the case was settled a year later for $7.5 million.