Britain's The Financial Times newspaper quoted Ukraine's prosecutor general on Friday as saying Kiev authorities had sold missiles to Iran and China.
The daily quoted Prosecutor-General Svyatoslav Piskun as saying 18 X-55 cruise missiles, also known as Kh-55s or AS-15s, were exported in 2001, when former President Leonid Kuchma was in power. But none were exported with nuclear warheads.
Piskun's office described the newspaper's account as untrue, drawing a distinction between formal export and what he described as smuggling.
"At issue in this interview is not the export of missiles but rather smuggling," a prosecution statement said, adding that the security services, the SBU, had an investigation underway.
"At issue in this interview is not the export of missiles but rather smuggling"
"The SBU has launched a criminal case against the director of the Ukraviazakaz firm, V Yevdokimov, in this connection. This case has been examined since August 2004 by the Kiev regional appeal court in closed session."
The affair highlighted the problems faced in imposing control on the Soviet legacy of military high technology, especially in core republics of the former Soviet military-industrial complex such as Ukraine.
It said two Russians were being sought and the extradition had been requested of a third held in the Czech Republic.
A Czech court is to hear arguments on whether Russian entrepreneur Oleg Orlov legally can be extradited to Ukraine. Orlov was arrested at Prague airport in 2004 while in transit.
Foreign Minister Borys Tarasyuk, speaking in Belarus, said the government in power after mass Orange Revolution protests "can only denounce past unauthorised transfers of arms".
"Ukraine's president and government have drawn conclusions and want to reorganise the system of export controls."
The Financial Times quoted the US embassy in Kiev as saying it was closely monitoring a Ukrainian government investigation into the case.