"In line with an official order received by the company, all Russian male citizens aged from 16-60 will be refused entry into Ukraine," Aeroflot said, adding that exceptions would only be made in extreme cases such as the death or illness of a relative.
The ban also applied to men aged 16-60 and women aged 20-35 travelling on Ukrainian passports registered in Crimea, which was annexed by Russia last month, Aeroflot added.
The Russian foreign ministry confirmed the ban in a statement, saying border guards at the country's main airports had told Russian airlines it was due to an order from security services. It called for an official explanation, saying Russia would consider reprisals.
Russia's other main carrier to Ukraine, S7, said it had not received the notice but its flights from Ukraine today were being delayed due to increased checks of passengers.
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"Now Ukrainian border guards have strengthened control over travellers arriving in Ukraine... To limit access to its territory for undesirable individuals," he said.
He said the measures were due to an operation by the Ukrainian government against pro-Russian separatists who have seized official buildings in the east of the country and the "risk of possible terrorist acts".
Ukraine's government has accused Russia of planning to invade eastern Ukraine and annex the territory following the seizure of Crimea last month.
A spokesperson for Russia's railway monopoly RZhD meanwhile said it had yet to receive the notice banning Russian males entry but acknowledged it was possible, Russian news agencies reported.