In the tape, Dr Kelly dismissed comments on Iraq's weapons capabilities made by Foreign Secretary Jack Straw and US President George Bush as "spin".
But he did not back up claims that Downing Street communications director Alastair Campbell was responsible for "sexing up" a Government dossier on Iraqi arms by demanding the inclusion of a claim that weapons of mass destruction could be launched within 45 minutes.
Newsnight reporter Susan Watts recorded the phone chat without Dr Kelly's knowledge the day after the controversial Radio 4 report made its claims.
The May 29 report on the Today programme was later revealed to be based on information given to its defence correspondent Andrew Gilligan by Dr Kelly, Britain's leading expert on Iraqi weapons of mass destruction programmes.
But Watts told inquiry chairperson Lord Hutton that there were "significant differences" between what Gilligan reported and what Kelly told her.
She told the inquiry: "He didn't say to me that the dossier was transformed in the last week and he certainly didn't say that the 45-minute claim was inserted either by Alastair Campbell or by anyone else in government.
"In fact, he denied specifically that Alastair Campbell was involved in the conversation on May 30... he was very clear to me that the claim was in the original intelligence."
Kelly had mentioned Tony Blair's chief "spin-doctor" in a separate conversation about the dossier earlier that month, but in a "gossipy, off-the-cuff, almost gratuitous" way which did not suggest he was offering an informed opinion, she said.
But she did not regard the scientist's comment as serious enough to report on Newsnight, and returned to it only after hearing Mr Gilligan's report on Today.
