In 2011, Mr. Babis founded his own political party, ANO (the name means “Yes” in Czech), and in the 2013 parliamentary elections, the party placed second, behind Mr. Sobotka’s Social Democratic Party. The parties formed an uneasy coalition, and Mr. Babis was named finance minister.

In January, the Czech establishment teamed up against Mr. Babis, enacting a law that would bar cabinet ministers from owning media companies or more than one-quarter of any company seeking government contracts or European Union subsidies.

Mr. Babis responded by declaring that he would place his business holdings in a trust.

The controversy involves corporate bonds that Agrofert issued in 2012 under a program that allowed buyers of the bonds to enjoy a tax exemption on the interest. Mr. Babis bought some of the bonds himself. The authorities are looking into how he obtained the money to buy the bonds, and whether he benefited improperly from the transaction.

Mr. Sobotka said that Mr. Babis had set a bad example.

“It is unacceptable for the finance minister not to be able to prove the origins of his property, especially since he is a member of a government that has built its program on a fight against tax evasion,” Mr. Sobotka said at the news conference. “It is impossible for the government to chase small entrepreneurs when a billionaire is evading taxes.”

Mr. Sobotka said it was a difficult decision.

“If I ask the finance minister to resign, I might turn him into a martyr in the upcoming months,” the prime minister said. “He has been preparing for that role for the past few days already. I chose the only possible decision.”