The vote threatened to damage relations between Russia and Ukraine, which, after months of squabbling over what to do with the fleet, had agreed to divide the force equally by 1995.
'I feel ashamed about this decision,' Mr Yeltsin said in the central Siberian city of Irkutsk, as he waited for the German Chancellor, Helmut Kohl, to arrive for two days of talks near Lake Baikal. 'The problems of the Black Sea fleet and the town where it is based must be solved calmly and gradually,' he said. 'Otherwise, what do you want me to do - fight with Ukraine?'
Mr Yeltsin is involved in a power struggle with parliament and is unlikely to pay the resolution much attention. But a fresh quarrel with Ukraine would be an unwelcome distraction as he struggles to draw up a constitution for Russia, which would give him considerably more power.
The vote elicited a predictably angry reponse from Ukraine. Volodymyr Kryzhanovsky, Ukraine's ambassador to Moscow, said yesterday that the resolution could be compared to 'Gavrilo Princip's shot in Sarajevo'. Princip, a Serbian revolutionary student, assassinated Archduke Franz Ferdinand of Austria-Hungary in Sarajevo on 28 June, 1914, triggering the First World War.
Tass said Mr Yeltsin also sharply criticised moves by three important Russian regions - Sverdlovsk, Chelyabinsk and the far eastern Primorsky Krai - to declare themselves republics.
The president needs the support of regional leaders to give final approval to a new constitution that would cut back parliament's powers while boosting his own. But some of the richer regions are now refusing to sign until they are granted the same law-making rights as the country's 20 ethnic republics.
Mr Yeltsin convened a special Constitutional Assembly last month to draw up the draft of the new constitution. The body is due to hold its final plenary session tomorrow.
Despite the dispute over the Black Sea fleet, Russia, Ukraine and Belarus agreed yesterday to form an economic union in an attempt to repair links shattered by the collapse of the Soviet Union. Itar-Tass news agency said the prime ministers of the three nations, meeting outside Moscow, had officially agreed on urgent measures to integrate their economies. They instructed experts to come up with a treaty for signing by 1 September this year.