David Abrahams has denied giving an interview in which he was quoted saying he donated cash secretly to avoid accusations of a "Jewish conspiracy".
Mr Abrahams says he remained anonymous to protect his privacy
Comments in the Jewish Chronicle were "misrepresented" and he had donated anonymously to protect his privacy, the businessman's spokesman told the BBC.
The Jewish Chronicle said it spoke to Mr Abrahams by phone and stood by the contents of the interview.
Police are probing £663,975 given to Labour by Mr Abrahams through proxies.
Mr Abrahams had been quoted in the newspaper defending himself against claims his money had come from Israel, saying it was "earned legitimately through hard work".
The newspaper also reported that he warned: "If the government starts hammering me, then it might take one or two dirty turns there as well."
But Mr Abrahams' spokesman, Martin Minns, said in a statement: "Reported comments in the Jewish Chronicle have been misrepresented.
"He wanted to remain anonymous to protect his privacy and for no other reason.
"All week he has refused to give the Jewish Chronicle an interview and this report warrants no further comment."
The editor of the Jewish Chronicle, David Rowan, told Newsnight the paper had talked to Mr Abrahams "by phone at the beginning of this week's news cycle and we have notes backing everything".
"He subsequently didn't grant a full one-to-one interview but we stand by everything," he added.
Mr Abrahams' donations were unlawful because people must use their own names when giving more than £5,000 to political parties.
Prime Minister Gordon Brown has said the party will pay all of the money back, and Labour officials have been holding talks with the Electoral Commission as to how this should be done.
Opposition parties have criticised Mr Brown's insistence that he knew nothing about the third-party arrangements.
Conservative leader David Cameron has said this "beggars belief", while the Liberal Democrats' acting leader, Vince Cable, called the scandal a "sleazy affair".
The disputed interview with Mr Abrahams is published in Friday's edition of the Jewish Chronicle.