Russian has allegedly used a tanker to block access to the Sea of Azov for Ukrainian naval vessels.
The incident flared up over the weekend in an escalation of tensions over the Russian-annexed Crimean peninsula.
Russia fired on and seized three Ukrainian vessels - two gunships and a tug named as Yana Kapa, the BBC reported.
Six Ukrainian crew members were injured, Ukraine said.
The trouble began when Russia accused the Ukrainian ships of illegally entering its waters.
The Russians then reportedly placed an unnamed tanker under a bridge in the Kerch Strait, which is the only access to the Sea of Azov, an area shared by the two countries.
Ukraine claims the tug was rammed.
Movement of ships through the Kerch Strait resumed on Monday morning, Ukraine’s Seaport Administration said.
A total of 30 vessels were waiting to pass through.
Russia's FSB confirmed that one of its patrol boats had used force to seize the three Ukrainian vessels, but said only three sailors had been wounded.
Ukraine said it had informed the Russians of its plan to move its ships through the sea to Mariupol.
