Tran Van Dung, 57, was sacked for "having committed serious violations and wrongdoings", the ministry said in a statement, without elaborating.
Dung did not respond to requests for comment.
The Southeast Asian country in March called for the anti-corruption drive to be stepped up, with a focus on financial markets.
A series of high-profile corporate arrests on accusations of market manipulation has triggered a $40 billion wipeout for Vietnamese stocks and rattled investor confidence in the fast-growing economy.
Earlier this week, the director general of the Hochiminh Stock Exchange was expelled from the Communist Party of Vietnam and authorities issued warnings to several other stock market officials for "violations."
(Reporting by Khanh Vu; Editing by Kanupriya Kapoor)
