Irving Picard is charged with clawing back billions of dollars for the victims of Madoff's Ponzi scheme and on Wednesday lodged new claims against several financial institutions, including three Swiss banks.
Banque Cantonale Vaudoise (BCV) said in a statement it "strongly disputes the basis of the action."
The request for $10 million issued by the liquidator concerns investors who sold Madoff funds via the BCV and "does not concern the bank directly", it said.
Private bank Lombard Odier & Co said in a statement it too "emphatically disputes the claim lodged by Picard and will employ all legal means available to challenge it."
The Geneva-based bank said it did not recommend investing in Madoff's funds, nor the "feeder" funds which supply them.
A third Swiss bank implicated in the affair, EFG International, declined to comment, saying it had not yet received a claim.
Wall Street financier Madoff succeeded for decades in convincing hundreds of investors that he was racking up huge profits with their savings.
Based on the fake profit reports they had received from Madoff's investment fund operations, victims claimed some $65 billion in losses after the business collapsed in December 2008.
Picard is claiming $355 million from EFG International, $180 million from Lombard Odier and $10 million from BCV, the Swiss news agency ATS reported.