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Dr Cullen said he had failed to fully disclose his interests, which became an issue earlier this year when Labour claimed a conflict of interest.
That was because he had asked parliamentary questions about the Government's planned buyback of the country's rail tracks while he still held shares in the rail operator.
But Mr Key said last night it had been public knowledge for months that his family trust had been shareholders in Tranz Rail until the shares were sold in June 2003.
He said the number of shares varied at different times and were managed by a broker who had authority to act without referring back to the trust.
"This attack by Michael Cullen and the Labour Party research unit is further evidence they will run a desperate smear campaign against me," he said.
When Mr Key was questioned on the issue this year he said his family trust had held 30,000 shares in the company, but sold them on June 9 and June 12, 2003.
He said his questions and comments never led to any gains from the company's share value.
But Dr Cullen yesterday released correspondence and share register information contradicting several of Mr Key's claims.
The information showed Mr Key, through his trust and under his own name, had owned 100,000 rather than 30,000 Tranz Rail shares.
Questioned on the issue before he was aware the information had been released, Mr Key told One News his shareholding ranged between 25,000 and 50,000 shares up until June 2003.
But when pressed on the issue he admitted there were more shares.
"Actually maybe 100,000 from memory, sometimes 50,000, sometimes 100,000, yep," he said.
"Yeah, sorry, there was 100,000 in total."
Mr Key said no one had questioned him previously on exactly how many shares he had owned.
Dr Cullen said Mr Key should have declared his shareholding to Parliament and his failure to do so was unethical.
"John Key lied because he knew he had something to hide," he said.