The incident flared up over the weekend in an escalation of tensions over the Russian-annexed Crimean peninsula.
"Having breached this morning the Russian border, the three Ukrainian ships - the Berdyansk, the Nikopol and the Yani Kapu - tried again on November 25 at 19:00 (Moscow time) to conduct illegal actions in Russian territorial waters", the FSB said on Sunday.
The statement said a group of Ukrainian Navy vessels were attacked by Russian coast guard ships as they were leaving the 12-mile zone of the Kerch Strait - which links the Sea of Azov and the Black Sea.
Russia's FSB security service said early on Monday its border patrol boats had seized two small Ukrainian armored artillery vessels and a tug boat after opening fire on them and wounding several sailors, the most serious clash between Moscow and Kiev in years.
But Russia said the ships were in its waters, and accused the Ukrainians of "provocative actions". FSB didn't mention ramming any vessels or tugboats.
"We need new sanctions against Russia", Ukraine's ambassador to the European Union Mykola Tochitsky said in a tweet on Monday.
All of this unfolded after three Ukrainian ships set sail from Odessa on their way to Mariupol, renewing tensions near Crimea, a region that Russian Federation annexed in 2014.More news: American missionary John Chau bore gifts for tribespeople
"Their goal is clear", an FSB statement said, "to create a conflict situation in the region".
Both countries have the right to use the sea, but following Russia's annexation of Crimea in 2014, Moscow controls both sides of the strait.
The statement added that Russia had been informed in advance about the planned transit, something Russia has denied, according to Russian news agencies.
A Reuters witness said Russia backed its blockade with at least two Sukhoi Su-25 warplanes which screeched overhead, while Russian state TV said Russian combat helicopters had been deployed in the area. He said he had called the meeting, "to discuss unsafe Ukraine provocations in the sea of Azov and Kerch Strait near Crimea threatening worldwide peace and security".More news: Match-saving magic from Tiger stuns golfing world
Russia is still fomenting rebellion in some breakaway provinces and Russian troops - despite denials by the government - are still in Ukraine.
The Ukrainian Foreign Ministry said in an earlier statement that Russia's actions were a violation of the UN Charter and worldwide law, and pledged to "promptly inform our partners about Russia's aggressive actions". It said the Kerch Straits had been closed for security reasons.
They spoke after Ukrainian president Petro Poroshenko scrambled the Ukrainian navy and convened a parliament vote on declaring martial law, while protesters fired smoke grenades and burned tyres outside the Russian embassy in Kiev.More news: Federal judge blocks Trump's asylum ban