Former prime minister and JD(S) leader HD Deve Gowda called Mr Thackeray yesterday and extended an invite for his son's oath-taking ceremony, Sena MP Sanjay Raut told PTI.
"However, Uddhavji politely declined and extended his best wishes to the new government," he said.
"Uddhavji told him he was very busy with the Palghar bypoll and hence, would not be able to attend the ceremony. These elections are very important for us," Mr Raut added.
The by-election to the Palghar Lok Sabha seat is scheduled to be held on May 28.
The Congress has 78 lawmakers in the lower house of Karnataka against 37 of the JD(S).
The BJP has dubbed the Congress-JD(S) alliance "unholy" and claims the government will not complete its full term.
It has decided to boycott today's oath-taking ceremony and said it will observe "anti-popular mandate day" to protest the formation of the coalition government in the southern state.