Ukraine's deputy foreign minister claimed an aircraft was "de facto hijacked" from Kabul airport before heading to Iran.
Confusion reigned on Tuesday amid conflicting messages over whether a Ukrainian plane had been hijacked in Afghanistan.
Yevgeny Yenin, Ukraine's deputy foreign minister, told the radio that the aircraft was "de facto hijacked" from Kabul airport on August 15, from where "it flew to Iran with a group of unknown passengers instead of evacuating Ukrainians".
Yenin's own foreign ministry then denied the claims.
Ministry spokesman Oleg Nikolenko told the AFP news agency that Yenin's claims "do not correspond to reality".
"There are no Ukrainian planes hijacked in Kabul or elsewhere," Nikolenko said.
The three planes -- two civilians and one military -- that Kyiv chartered to evacuate its nationals from Afghanistan "returned to Ukraine in safety" carrying a total of 256 passengers on board, he added.
A source in the Ukrainian government told AFP that the aircraft mentioned by Yenin was being negotiated with a view to its possible participation in the operation to evacuate Ukrainian nationals, but this project had failed because the aircraft had left Kabul without warning last week.
"We wanted to charter it, but he left without taking anyone," the source added. "Nobody hijacked it," she said without being able to specify the destination of the plane or the exact date of its departure.
Ukraine has so far organised three evacuation flights that left Kabul on August 15, 21 and 23, including Ukrainians and Afghans, including director Sahraa Karimi, star of independent Afghan cinema.