In Kiev, Ukraine's parliament also was deliberating on a plan to impose martial law for a period of 60 days, which would keep its military forces at a heightened state of readiness.
"The National Security and Defense Council's decision concerning "emergency measures to ensure Ukraine's state sovereignty and independence and declare martial law in Ukraine" is hereby enacted", President Pyotr Poroshenko announced on his website.
Arsen Avakov described it as a an act of aggression that "will be used as proof in worldwide court".
The escalating crisis came amid worldwide outrage over the incident in the Kerch Strait, with European Council President Donald Tusk condemning Russia's "use of force" and demanding it "return Ukrainian sailors, vessels and refrain from further provocations".
"All hell broke loose" as the Russian Coast Guard opened fire on the Ukrainian ships, which were awaiting assurances of safe passage through the strait, said Volodymyr Yelchenko, Ukraine's ambassador to the United Nations, at the emergency session of the Security Council. Russian media say three were injured. The trio of Ukrainian ships were taken to port in occupied Crimea and have been held there along with 23 Ukrainian sailors.
Dominique Arel, an expert in Ukrainian studies at the University of Ottawa, said the chances of the West taking military action are slim, just the likelihood of further sanctions might be. Since Russia annexed Crimea, tension has risen with both countries complaining about shipping delays and harassment.
The city, with a mixed Ukrainian-Russian population, is located on the north coast of the Sea of Azov close to the border with Russia.
Sunday's incident was a dramatic increase in tensions between the two countries, almost five years after Russian Federation invaded and seized the Ukrainian peninsula Crimea and began sending arms and troops to lead a separatist movement in eastern Ukraine.
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Three gunmen tried to enter the consulate in the southern port city, but were intercepted by guards at a checkpoint. Mohammad Ashfaq, a local police chief, says more than two attackers stormed the consulate on Friday.
Russian Foreign Minister Sergei Lavrov on Monday accused Kiev of "dangerous" moves in the Kerch Strait after a confrontation between Russian and Ukrainian navy ships.
Separately, the International Monetary Fund said introducing martial law would have no bearing on continued IMF cooperation with Ukraine.
The conflict ended with the capture of the enemy ships that are now trapped in Russian territorial waters.
The passage has also reportedly been blocked by a Russian tanker ship with no indication of when it will move.
Russia's Federal Security Service (FSB) said it used weapons after the Ukrainian ships ignored demands to stop and that it impounded three vessels which had illegally crossed the border. Commenting on Facebook, Russian Foreign Ministry spokeswoman Maria Zakharova called the events a "provocation" and accused Ukraine of setting it all up to accuse Russia of aggression.
Moscow is able to control access between the Sea of Azov and the Black Sea after it built a bridge that straddles the Kerch Strait between Crimea and southern Russian Federation. The EU has called for de-escalation.
Two Su-25s Frogfoot ground attack aircraft, armed with an anti-ship payload (either Kh-31 or Kh-35 anti-ship missiles), were scrambled by the Russian military to support the navy operations. Crimea, on the western shore, is now controlled by Moscow, the eastern shore is Russian territory, and the northern shore is controlled by Ukraine.