Ukraine on Thursday opened a criminal probe into an incident in which it said one of its military planes was shot at over the Black Sea, but which Moscow condemned as a "dangerous flyby".

The general prosecutor in Kiev said in a statement that an attempted murder case had been launched after a Ukrainian Antonov-26 transport aircraft was shot at Wednesday during a training flight over the Black Sea, where Russia operates drilling rigs it took over following its annexation of Crimea in 2014.

The fuselage of the plane -- which Kiev insisted was over Ukrainian waters -- had a three-centimetre (1.2 inches) bullet hole, but its crew were not injured in the incident, Defence Minister Stepan Poltorak said Wednesday.

Russia's defence ministry said late Wednesday that it had summoned Kiev's military attache in the country to complain over what it said were "two dangerous flybys at an extremely low altitude" over the drilling platforms.

"The actions of the Ukrainian plane are viewed as provocative," defence ministry spokesman Igor Konashenkov said.

The incident comes after an upsurge in clashes between pro-Russian separatists and Ukrainian forces in eastern Ukraine that has left a reported 21 people dead since Sunday.

The fresh clashes in the industrial town of Avdiivka are the worst violence to hit the war-torn region in months.

Russia annexed the Black Sea peninsula of Crimea from Ukraine in March 2014, sparking international condemnation.

Since then, a conflict between government troops and Russian-backed rebels in Ukraine's east has left nearly 10,000 people dead.

Since the annexation of Crimea, Russia has taken over Ukrainian companies in the region, including energy company Chernomorneftegaz which runs drilling operations in the Black Sea.