Ukraine says the move violated the 2003 agreement between the two nations on treating the Sea of Azov and the Kerch Strait as shared waters without any restrictions.
The Kremlin claimed the Ukrainian ships entered Moscow’s territorial waters without submitting the correct transit applications that Russia introduced in recent months to “ensure safe navigation”.
Amid a threat of “full-scale war”, Western governments have rallied behind Kiev, accusing Russia of illegally blocking access to the Sea of Azov and using force without justification.
What is the dispute about?
The territory Moscow accuses Kiev of violating on Sunday is a 12-nautical-mile strip in the Black Sea off the coast of Crimea that Russia says belongs to it since the peninsula’s annexation.
“One should remember that Russia’s attempted annexation of Crimea has not been recognised by any state in the world, so Russia cannot pretend it has full control over the naval border,” Olexiy Makeyev, the Ukrainian foreign ministry’s political director, told Al Jazeera.
Ukraine said the vessels were not even in the disputed waters but in international waters when a Russian patrol ship blocked their way.
Kiev published a map on Wednesday showing where the standoff occurred, it caused a crash, seizure of all three Ukrainian vessels and the capture of 24 Ukrainian crew members.
The strait that connects the Black Sea to the Sea of Azov has significant political, military and economic importance for Ukraine.
Losing access to it would cut off the ports of Ukraine’s Mariupol and Berdyansk cities from the Black Sea, essentially turning the Sea of Azov into a backwater for the country.
The scenario would “increase the price of Ukraine’s exports” as its shipments would have to be redirected to different ports, Pavlo Kukhta, deputy chairman of Strategic Advisory Group at the Cabinet of Ministers of Ukraine, told Al Jazeera.
“Mariupol region exports a quarter of Ukraine’s metals,” he said.
It would also prevent Ukraine from going ahead with its plan to set up a naval base in the Sea of Azov, which was announced by President Poroshenko in late September.
Battling to regain its share of control over the Kerch Strait also has a symbolic political importance for the Ukrainian government, as it can do little to bring Crimea back into its fold.
For Russia, on the other hand, the Kerch Strait and the bridge that was hastily constructed over it after the annexation represent the only physical link between Russia and Crimea.
Follow Al Jazeera’s Tamila Varshalomidze on Twitter: @tamila87v