Ukrainian naval commander Sergei Haiduk was detained on Wednesday after his base in Sevastopol was taken over by pro-Russian forces.
An unidentified official in the Sevastopol prosecutor's office told news outlet Kryminform that Rear Admiral Haiduk was temporarily detained after he received an order from Kiev to use weapons against civilians, Itar-Tass reported.
The Ukrainian naval base in the Crimean city was seized by unarmed pro-Russian men who then raised the Russian flag on the square by the headquarters Wednesday morning, The Associated Press reported.
The unarmed men met no resistance and were later joined by Russian-speaking troops with no insignia on their uniforms.
There has been some confusion surrounding the circumstances of Haiduk's detention. Itar-Tass reported that Haiduk and around 50 soldiers left the base freely Wednesday morning, but other media outlets reported that the admiral was taken away in a car or led away in handcuffs.
Haiduk's whereabouts are still unknown.
It was also unclear how many Ukrainian servicemen remained at the headquarters.
On Tuesday, President Vladimir Putin signed an agreement to annex Crimea and Kremlin spokesman Dmitry Peskov said that Ukrainian troops must join the Russian army or leave the breakaway region.