Pro-Russian forces seized the Ukrainian naval headquarters in Sevastopol on Wednesday, a day after a Ukrainian soldier was shot dead, the first casualty of Russia's annexation of Crimea.

After Vladimir Putin announced on Tuesday that Russia would absorb Crimea into its fold, attention now turns to the remaining Ukrainian military facilities on the peninsula.

On Wednesday morning, irregular local militia members entered the naval headquarters, which was then paid a visit by the head of Russia's Black Sea Fleet. Shortly afterwards, a number of Ukrainian soldiers walked out looking solemn, carrying their belongings in plastic bags.

A representative of the so-called self-defence units said they had carried out an operation to liberate soldiers held captive. "We wanted to set free the prisoners in the base that are being illegitimately held there by their commander," said Vladimir Melnik, who said he was the head of a local self-defence unit. He said a criminal case would be opened against the commander.

In Kiev, the Ukrainian prime minister, Arseniy Yatsenyuk, who on Tuesday announced that the conflict with Russia had moved to a "military phase", said he was dispatching his deputy, Vitaly Yarema, and the acting defence minister, Ihor Tenyukh, to Crimea to "resolve the situation".

However, Crimean authorities said the mission would not be allowed into the territory. "Nobody wants them in Crimea. Nobody will let them in, they will be sent back," said the region's de facto leader, Sergei Aksyonov, according to Interfax.

A large number of Ukrainian soldiers have defected or deserted but there are some who say they will fight rather than leave their posts. However, the situation in Sevastopol on Wednesday was further confirmation that few soldiers have any desire to engage in a firefight with the Russians.

The Russian parliament is likely to vote on the absorption of Crimea by Russia on Wednesday, a day after Putin gathered the Russian political elite in the Kremlin for a searing speech in which he criticised the hypocrisy of the west and said Russia was acting no differently from the US.

In the hour-long speech, likely to go down as one of the defining moments of his long rule over Russia, Putin said western politicians "call something white today and black tomorrow" and aired a long list of foreign policy grievances going back to 2000, saying "we were cheated again and again, with decisions being taken behind our back".

Diplomacy over the Crimea land grab continues to be fraught, with Russia and the EU trading accusations over a supposed trip to Moscow by the European Council president, Herman Van Rompuy. Sources in Brussels said the trip had never been agreed, but the Russian foreign ministry said in a statement that Van Rompuy had "invited himself" but was then banned from coming "by his own side".

The foreign ministry claimed that the Europeans did not want to hear the real version of events on Crimea: "Why would he need to know the truth if everything has already been decided?"

The US vice-president, Joe Biden, speaking during a visit to Poland and the Baltic states aimed at assuring Russia's EU neighbours about US and Nato security guarantees, said on Tuesday that Putin and Russia stood alone and "naked before the world", guilty of international aggression.

"Russia has offered a variety of arguments to justify what is nothing more than a land grab," he said. Biden revealed that the US was considering deploying ground troops to the Baltic states on new military exercises as it seeks to reassure Nato allies in eastern Europe of its commitment to preventing further territorial aggression by Russia