The ministry made the decision late on Friday after the PSSI continued to ignore its recommendation to suspend two clubs from competing in the domestic soccer league because of ownership concerns.
On Saturday, despite the ban, La Nyalla Mahmud won 92 of 106 votes to replace Djohar Arifin and run the PSSI until 2019 at a congress in Surabaya where fans of Persebaya -- one of the clubs that the government wanted banned -- protested outside.
"We will fight against the government's decision because only FIFA has the right to dissolve PSSI. We bow to FIFA regulations," La Nyalla told The Jakarta Post.
The actions of the ministry are in breach of the regulations set out by world governing body FIFA, who demand no government interference in the running of sport by local football associations.
FIFA had already warned the Indonesian government to stay away from local football matters after the start date of the domestic league -- currently suspended because of the row -- was pushed back six weeks while clubs underwent further checks.
Indonesia now risk being banned from competing internationally which would jeopardise their 2018 World Cup and 2019 Asian Cup qualifying campaign which begins in June.
(Writing by Patrick Johnston in Singapore; editing by Sudipto Ganguly)
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