Jan Dziedziczak, a government spokesman, speaking to PAP news agency, said: "The decision is based on facts revealed by the Central Anti-Corruption Office regarding large-scale corruption."
He said two people had been arrested in connection with the investigation.
The prime minister's office later issued a statement saying Lepper had been dismissed from both his post as deputy prime minister and agriculture minister.
As part of a different corruption investigation, the prime minister also fired Tomasz Lipiec, Poland's sports minister, of his Law and Justice party.
Early elections
The surprise move threatens to deprive Kaczynski of a majority in parliament and prompt early elections two years after the Law and Justice party formed an uneasy alliance with Lepper's party and another nationalist party.
A senior Law and Justice source said Kaczynski would seek to keep Samoobrona in government, but Lepper said his party would leave.
Speaking on Polish TVN24 television, Lepper said: "Samoobrona will not take part in such government. In such a case, I believe there will be early elections."
He denied any wrongdoing, saying the corruption inquiry apparently regarded some land deals.
Asked why he had been sacked, he said: "I don't know. I need to sleep on it."
The three-party coalition has been rocked by infighting since its inception, but few analysts expected it to break up before the next election, due in 2009.
"There could be early elections," Marek Migalski, a sociologist at Silesia University, said. "They don't have to happen immediately - we may go through a minority government."
Kaczynski has sacked Lepper before, after clashes over the budget last autumn, but was forced to bring him back into the cabinet in October to end a three-week political crisis and avoid the risk of snap elections.