"This claim simply isn't serious and its only motive is a political one," said Olexander Turtshinov, head of the SBU domestic security and intelligence service.
"The enquiry into the missiles sale has been carried out by the SBU and we found Yushchenko shouldered no responsibility in the matter," insisted Turtshinov.
"We are prosecuting all the people involved and we shall bring all of them to court," he said.
Member of parliament Taras Chornovil said Saturday that a deal in 2001 "took place when Yushchenko was prime minister," and "the transaction could only take on such dimensions after arrangements with the prime minister who knew" about it.
Yushchenko headed the Ukrainian government between December 1999 and April 2001 before joining the opposition to then president Leonid Kuchma and becoming president late last year.
He has admitted that nuclear-capable cruise missiles were sold illegally to China and Iran under Kiev's previous regime but said the X-55 missiles were exported under a forged contract that had Russia as the country of destination.
No nuclear warheads were sold with the missiles, made in 1987, which have a range roughly of 3,200 kilometers (2,000 miles) and were poorly maintained, according to a Ukrainian source familiar with the investigation.
According to Ukrainian public prosecutors the sales were illegal and could not be considered Ukrainian exports.
Six missiles were sold to Iran in 2001 and six to China, they have said.