Lepper said the coalition "was broken by Kaczynski's party", which last week appointed a controversial farm minister over Samoobrona's protests.
The minister, Wojciech Mojzesowicz, quit Samoobrona in 2002 and is now a member of the conservative PiS.
He angered his former colleagues last year by trying to persuade some of them to jump ship in exchange for top political posts.
Kaczynski has accused Samoobrona of intransigence over Mojzesowicz's appointment, and said: "If our allies want to break it [the coalition] up, we will have a minority government, followed by a snap election."
The next election is not formally due until 2009.
The Polish parliament is in summer recess so the effects of Samoobrona's decision - passed in a vote of 61-8 - will not be felt for some weeks.
Lepper said that the two ministers affected - Anna Kalata, the labour minister, and Andrzej Aumiller, the public works minister - "are currently on leave, and they'll put themselves at Prime Minister Kaczynski's disposal after the vacations".
He said his party "would not vote any more in line with PiS policies from the next parliamentary session, which starts on August 22".
Karol Karski, a PiS MP, was sceptical.
"Let's wait and see if Samoobrona's ministers really offer their resignations and how its MPs vote in parliament at the end of the day," he said.
The PiS - which is run by Kaczynski and his twin brother Lech, who is the country's president - has just 150 MPs in the 460-seat parliament.
It governs through a coalition with Samoobrona, which held 44 seats, and the League of Polish Families (LPR), which has 29.
The LPR's leadership is to meet on Monday to decide whether it will continue to support the PiS.
Lepper said his party, which was formed from a rural protest movement in the 1990s, intended to continue to work with the LPR through an alliance both have recently forged.
Lepper himself was sacked as deputy prime minister and farm minister in July amid bribery allegations and implication in a political sex scandal.