Dinh La Thang, a serving member of Vietnam's 19-member Politburo -- the party's top decision-making body -- was fired over his previous stewardship of PetroVietnam, the party said in a statement.
"He made both mistakes and very serious violations during his management and leadership... Badly influencing the prestige of local party organisations," the statement said.
Multiple top officials have been prosecuted for corruption and incompetence at Vietnam's graft-ridden state- run firms but Thang is one of the most senior party officials to have fallen from grace in years.
Thang was chairman of the board at PetroVietnam from 2006 to 2011 and was later promoted to transport minister.
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He became a Politburo member in 2016 and was also made head of the party in Ho Chi Minh City, the country's southern commercial hub formerly known as Saigon.
The Communist Party Inspection Committee accused Thang of allowing PetroVietnam to make loans to the private Ocean Bank that caused "serious losses" to the company.
Vietnam has been struggling to clean up its vast and inefficient state-run sector for years.
There have been a string of high-profile arrests and prosecutions of wealthy businessmen and executives in recent years.
But analysts say they are more often the result of political infighting rather than a genuine commitment to reform.
It is not the first time PetroVietnam has come under scrutiny.
Last year four senior employees at a construction subsidiary of the firm were prosecuted for mismanagement that allegedly cost the company USD 150 million.
That year a court also convicted the former chairman of Vietnam Construction Bank and 35 other employees for stealing more than USD 400 million from the joint-stock bank.