More than 300 Ukrainian troops have crossed into Russia during heavy fighting with pro-Russian separatists.
A Ukrainian security spokesman, Andriy Lysenko, said the 311 soldiers and border guards "had to cross into Russian territory" at the Gukovo checkpoint in eastern Ukraine.
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 defence 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 Mr Lysenko, spokesman for Ukraine's National Security and Defence 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 motorised brigade.
Recently Kiev has been gaining ground against the rebels and claims to have retaken more than 60 towns in Donetsk and Luhansk.
Preparing for siege
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.
Meanwhile, more than 100 experts from the Netherlands and Australia have continued searching the crash site of Flight MH17, in a rebel-held area close to the fighting.
More human remains and belongings from the Malaysia Airlines jet shot down last month were flown to the Netherlands on Monday.
Remains of more than 200 victims have been transferred to the Netherlands for identification. Up to 80 bodies are believed to be still at the site.
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.
Announcing the air force exercise, the Russian defence ministry said it would involve Sukhoi Su-27 and MiG-31 fighter jets, Mi-24 and Mi-28 helicopters and Russia's newest frontline bomber, the Sukhoi Su-34.
Every time Russia announces a new round of military exercises it is seen as a show of strength in the conflict with Ukraine, a BBC correspondent says.
The spokesman told Interfax news agency that the exercise was the first in a series intended to improve the unity of the air force.
Russia has previously been accused of boosting its troops and weaponry along the border with Ukraine.