Christoph Mueller was picked last year to rescue the airline after it was hit by two disasters in 2014 involving its planes.
But yesterday he said he was leaving before the end of his three-year contract for unspecified "personal reasons".
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"It's like now there is a huge crack in the ship and when there is a leak, all hell will break loose again," it said, warning darkly of "another chapter of leakages."
Malaysia Airlines had run up huge losses for years but was pushed to the brink of bankruptcy after a terrible 2014.
Flight MH370 disappeared in March that year with 239 passengers and crew aboard, and four months later MH17 was blown out of the sky by a suspected ground-to-air missile over Ukraine, killing all 298 passengers and crew.
Mueller's departure has sparked speculation over why he would leave a year after launching a drastic rescue plan in which he slashed thousands of jobs and trimmed the airline's route network.
Mueller earned the nickname "The Terminator" following previous restructurings of other airlines that also involved hefty job cuts.
One of his plans was to seek the renegotiation of unfavourable contracts with service providers and suppliers, which analysts have said likely raised hackles with politically connected Malaysian businesses.
The first-ever foreign boss of Malaysia's flag carrier had been hampered by "legacies and politics", the union said, adding that some of the German's decisions and proposals were dropped "without proper consultation (with) Mueller."
A Malaysia Airlines spokesperson could not immediately be reached for comment.
Aviation analysts have long blamed Malaysia Airlines' failure to stay competitive on unwise business decisions including over-reaching on long-haul routes, unfavourable supplier contracts, and government meddling.
State investment fund Khazanah Nasional, which took over the airline in late 2014 and is now its sole shareholder, has also been criticised in the past for poor management, including picking a revolving-door of past CEOs who lacked aviation industry experience.
Aviation analyst Shukor Yusof of Endau Analytics said he believed Mueller likely struggled against "the mindset of Khazanah," adding that deep structural problems remained.
"The structural problems cannot be solved until there is the political will to change the shareholder. They cannot have Khazanah," he said.
Mueller had previously helped turnaround Irish flag carrier Aer Lingus and occupied top positions at German national carrier Lufthansa and the former Belgian airline Sabena.
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