He will officially resign next Wednesday, Air France-KLM said.
Recently, Air France launched its own low-priced airlines in order to better compete with cheaper flight options.
Air France-KLM boss Jean-Marc Janaillac announced his resignation Friday after staff at the carrier's French operations rejected a pay deal aimed at ending weeks of strikes.
"If Air France does not make efforts to become more competitive, allowing this flagship to be at the same level at Lufthansa and other airline companies, Air France will disappear", Le Maire told BFM television. Air France-KLM had a negative net margin of 1.13% and a positive return on equity of 38.04%. research analysts forecast that Air France-KLM will post 2.71 earnings per share for the current year.
Meanwhile, Air France crews and ground staff were on their 13th day of striking on Friday.
The past quarter was substantially poorer because of the ongoing strike action at Air France where staff are demanding fatter pay packages.
Some worker representatives hit back at Le Maire on Sunday, after he called their demands unjustified. "I think we can find a way out".
"As a result, the pay agreement proposal of April 16 ensuring a 7% wage increase over 4 years, including a 2% increase in 2018, is no longer valid", the company said, and Janaillac is following through on his promise to be personally accountable. "There's reason enough to be anxious", CFDT leader Laurent Berger.
Labour reforms launched by French President Emmanuel Macron have also led to strikes by employees of the state-owned SNCF rail company.
Representatives from Air France unions are due to meet on Monday.
French Prime Minister Edouard Philippe has hailed Janaillac's "courageous" decision while calling on both sides "to assume their responsibilities".