Thomas Cook boss apologized after a video came out of staff who applauded him and other CEOs at the Condor branch after providing rescue assistance.
The German government intervened to save the business while Thomas Cook's workers lost their jobs.
"I have never, ever intended to commit a crime or appear inappropriate," said Jean Christoph Debuss, chief airline officer at the company.
Germany borrows Condor 380 million euros (336 million British pounds).
"I'm heartbroken that one of my colleagues thinks I was, and I'm really sorry about that," he added in a LinkedIn post.
The video was shot after a message from the German government, he said.
"The reaction of me, Condor management and employees was a relief that Condor could continue to fly and prevent more layoffs within Group Airlines. However, I realized that this video was inappropriate for the weather and I'm sorry. . "
In LinkedIn, former employees criticized his focus on Condor on the rest of the business.
" I'm sorry, Christoph, but it looks like you've sacrificed UK businesses to keep others going. " , writes Tom Williamson, who says he has worked for the company for 1
"The question is, where are our hard paid salaries?" asked Lee Lockhart, a cabin crew member.
"Obviously state aid is not authorized by the EU, but the UK appears to be the only country to take any notice," says Carl Plummer, a former pilot of the firm.  Impact of the collapse of Thomas Cook on the world
But he received some support: "Unfortunately you cannot please everyone, thank you for saving Condor," writes Jochen Heidenberger, travel agent.
Thomas Cook went into liquidation earlier this week, leaving thousands of passengers in line and 9,000 workers in the UK jobless. The company had asked for £ 250m from the UK government to continue operating, but this was refused as the government claimed it would not survive anyway.
"Thomas Cook's directors must explain why the UK airline should be closed, but German was allowed to continue operating," said Balpa Pilot Union Secretary General Brian Sturton.
"How was it funded because it appeared that there was nothing left for the UK staff in the cash registers? And why couldn't the UK government give the same kind of bridge support as the German government when it was well known that Thomas Cook Chinese buyer was lined? This is a national scandal. "