"This deal (...) took place when Yushchenko was prime minister," Interfax-Ukraine news agency cited member of parliament Taras Chornovil as saying.
"The transaction could only take on such dimensions after arrangements with the prime minister who knew" about it, he added.
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.
The deputy said press reports that the president's brother, Petro Yushchenko, was involved in the weapons smuggling were alarming.
A spokeswoman for Yushchenko denied the deputy's charge.
"Mr. Chornovil's statements are irresponsible and unfounded and only demonstrate his lack of maturity as a politician," the spokeswoman, Irina Gerashchenko, told AFP.
Iran has denied that Kiev delivered missiles capable of carrying nuclear warheads.