Pro-Russian self-defence forces have entered the Ukrainian navy's Black Sea headquarters in Sevastopol and raised the Russian flag above the building less that 24 hours after Vladimir Putin announced the annexation of Crimea in a searing speech to political elites in Moscow.

In an hour-long speech in the Kremlin on Wednesday – 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".

Crimean authorities have said that all Ukrainian military installations on the peninsula, including several bases, are now illegal and the soldiers must leave. Many have done so, but some remain.

Ukrainian and Russian troops had agreed a ceasefire until Friday, and the circumstances of the shootout on Tuesday remain murky

Russia's foreign ministry later denounced the decision of the president of the European council to cancel a visit to Moscow as a refusal to "hear the truth". Herman Van Rompuy had been due to meet Russian officials on Wednesday. Russia's foreign ministry said in a statement on Wednesday that Van Rompuy "was not allowed" to come to Russia "by his own people". The statement said Moscow had promptly reacted to his request to visit Russia but it was cancelled at the last moment by the European side.

The White House spokesman, Jay Carney, earlier foreshadowed a fresh round of sanctions against the Russian hierarchy. "More is coming," he said amid criticism that existing steps taken by the US and EU are too weak.

Carney suggested that powerful oligarchs with ties to Putin would be targeted. "I think anyone who understands how the Russian system of governance works and who has influence in that system understands the kind of person that we're talking about here, and the fact that they have substantial assets, not just in Russia but abroad," he said.

In his speech to the Russian parliament, Putin ridiculed the idea that events in Crimea amounted to Russian aggression and said there had been no shots fired and no casualties during recent weeks. Yet hours after he spoke, a Ukrainian soldier was shot dead at an army base in the Crimean capital, Simferopol, the first military fatality on the peninsula since the crisis began.

Ukrainian military sources said one junior officer had been killed and another injured by a sniper after an assault on the base by "unknown forces, fully equipped and their faces covered".

Arseniy Yatsenyuk, Ukraine's prime minister, accused Moscow of committing a war crime and said the conflict with Russia was "moving from a political to a military one". After the incident, Kiev issued a statement authorising its armed forces to use weapons to defend themselves.

Russia has also announced that the signatories of a 2011 Organisation for Security and Co-operation in Europe (OSCE) agreement had exhausted their quotas to inspect Russian military facilities and a planned inspection in the coming days would be the last.

"This is the last inspection held on the territory of the Russian Federation in 2014 under the Vienna Document because all quotas for inspections on our territory by OSCE states have been exhausted," said Sergei Ryzhkov, head of the national nuclear risk reduction centre.

Ukrainian inspectors would carry out the last checks.

According to the OSCE site, the agreement stipulates that 90 inspections and 45 evaluation visits can be conducted on the territory of any participating state that has armed forces each year.

On Monday, the US and EU announced sanctions against several top Russian officials. Van Rompuy and José Manuel Barroso, head of the European commission, dismissed Putin's case for annexation and pledged a "unified European response" at the EU summit in Brussels on Thursday, following the EU's decision to impose travel bans and asset freezes on 21 Russian and Crimean figures.

In Britain, the foreign secretary, William Hague, announced the suspension of joint naval exercises with Russia and of export licences for military items to Moscow, saying Putin had chosen the "route of isolation".

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 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.

The death of a Ukrainian soldier was a reminder that there is potential for Russia's annexation to turn bloody. Russian soldiers have been active in Crimea in recent weeks, despite Kremlin claims to the contrary, and often act in consort with local informal militias. There were reports that a local militia member had also been shot dead in the clash and another injured.

The White House called for an emergency meeting of the G7 countries on Ukraine to be held on the fringes of a summit in The Hague devoted to nuclear security. Russia is also invited to the summit, raising the possibility of a first face-to-face confrontation between Putin and western leaders in the crisis.