"I will shortly present my resignation to President Milos Zeman. It is unacceptable for Andrej Babis to stay on as finance minister," said Sobotka, in an announcement six months before an October election.
"I want to free the hands of coalition parties so they can launch negotiations on a solution to the situation or agree on the organisation of earlier elections," he added.
Presidential spokesman Jiri Ovcacek declined immediate comment. Under the Czech constitution, there is no deadline for the president to accept the government's resignation.
Contacted by AFP, political analysts in Prague said that an early election was unlikely to be called during the summer, pointing instead to the possibility of a minority caretaker government being installed until the October ballot.
Ranked by Forbes as the Czech Republic's second most wealthy citizen, Babis ran the sprawling Agrofert conglomerate before putting his assets into a trust earlier this year to ward off conflict of interest allegations.
Babis has alleged that Interior Minister Milan Chovanec, a member of Sobotka's CSSD, ordered police to investigate his business dealings, an allegation the minister has flatly denied.
Babis who has ruled out any wrongdoing, is riding high in opinion polls, with ANO scoring 33.5 percent support compared to just 16 percent for Sobotka's CSSD in a survey conducted by the CVVM pollsters in April.
Babis is also the Czech Republic's most popular politician with a 56 percent approval rating according to another April survey by the CVVM pollsters, compared to 39 percent and sixth spot for Sobotka.
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