A Ukrainian security spokesman, Andriy Lysenko, said the 311 soldiers and border guards “had to cross into Russian territory”.
Ukraine is trying to get them back now through diplomatic channels, he said.
Earlier a Russian security official said 438 Ukrainian troops had been given refuge in Russia as “defectors”.
The border area is very tense amid Ukrainian allegations that Russian forces have been helping the separatists with rocket barrages.
Russia has announced that it will hold an air force exercise this week near the border. A Russian defense ministry spokesman said 100 aircraft would take part in the operation.
The Russian foreign ministry meanwhile accused Ukrainian forces of deploying tactical missiles and launchers near the city of Donetsk
In his statement on the Ukrainian troops at the border Andriy Lysenko, spokesman for Ukraine’s National Security and Defense Council (SNBO), dismissed Russia’s claim that the troops had defected.
He also denied reports that the separatists had captured some Ukrainian National Guard servicemen during the fighting.
Another Ukrainian military spokesman said the group of soldiers had retreated into Russia after running out of ammunition and other supplies during the fighting. He said they belonged to the 72nd motorized brigade.
Recently Kiev has been gaining ground against the rebels and claims to have retaken more than 60 towns in Donetsk and Luhansk.
Civilians are preparing for a siege as government forces close in on the rebel-held cities of Donetsk and Luhansk.
Residents are stockpiling food and supplies and are sleeping in basements, with reports suggesting Luhansk is virtually surrounded and without power.
Western governments and Ukraine accuse Russia of supplying heavy weapons and volunteers to the pro-Russian rebels, who have declared independence from Kiev.
Russia denies supplying such hardware to the rebels, while condemning Kiev’s military offensive in the east.
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