Crimea's regional parliament has declared independence and applied to become part of the Russian Federation, a day after people in the Black Sea peninsula voted overwhelmingly to leave Ukraine in a referendum that most of the world has condemned as illegal.

The parliament "made a proposal to the Russian Federation to admit the Republic of Crimea as a new subject with the status of a republic", according to a statement on its website.

A Crimean parliamentary delegation was expected to arrive in Moscow on Monday to discuss the procedures required for the region to become part of the Russian Federation. Final results showed that 96.8% of voters were in favour of joining Russia, the head of the referendum commission said. Mikhail Malyshev told a televised news conference that the commission had not registered a single complaint about the vote.

Russia's lower house of parliament will pass legislation allowing Ukraine's southern Crimea region to join Russia "in the very near future", news agency Interfax cited its deputy speaker as saying on Monday morning.

"Results of the referendum in Crimea clearly showed that residents of Crimea see their future only as part of Russia," Sergei Neverov was quoted as saying.

Meanwhile, Ukraine's interim government has endorsed a presidential decree to carry out a partial mobilisation involving 40,000 reservists. Andriy Paruby, secretary of the National Security and Defence Council, told parliament that 20,000 reservists would be deployed in the armed forces and the rest in the newly created National Guard.

The speaker of the Crimean regional parliament said Ukrainian soldiers on the peninsula would be able to choose whether to side with the new separatist state or leave.

"The personnel of Ukraine's armed forces will be given an alternative: serve in Crimea and swear allegiance to the republic, or continue outside the borders of Crimea in the Ukrainian army," said Volodymyr Konstantynov.

The US and its allies in Europe are expected to announce sanctions against Russia, including visa bans and potential asset freezes.

The US president, Barack Obama, told his Russian counterpart, Vladimir Putin, on Sunday that Crimea's vote "would never be recognised" by the United States, as he and other US officials warned Moscow against making further military moves toward southern and eastern Ukraine.

The White House said Obama "emphasised that Russia's actions were in violation of Ukraine's sovereignty and territorial integrity and that, in co-ordination with our European partners, we are prepared to impose additional costs on Russia for its actions".

Obama told Putin the crisis could still be resolved diplomatically, but said the Russian military would need to first stop its "incursions" into Ukraine, the White House said. Putin told Obama the vote was "fully consistent with the norms of international law and the UN charter", according to a statement on the Kremlin website.

The European Union also condemned the referendum as illegal and said it was taking steps to increase sanctions against Russia. EU foreign ministers will meet on Monday to decide whether to impose asset freeze and visa sanctions and, if so, whom to target.

"The referendum is illegal and illegitimate and its outcome will not be recognised," Herman Van Rompuy, president of the European council, and José Manuel Barroso, European commission president, said in a joint statement on Sunday.

France and Germany echoed the statement by the British foreign secretary, William Hague, that Moscow must face "economic and political consequences".

Valery Ryazantsev, head of Russia's observer mission in Crimea and a lawmaker from the upper house of the Russian parliament, said on Monday that the results were beyond dispute. He told Interfax there were "absolutely no reasons to consider the vote results illegitimate".

Earlier on Sunday Russia and Ukraine agreed a truce in the region until Friday, Ukraine's acting defence minister announced, in a move that may ease tension between Moscow and the western-backed government in Kiev. Speaking on the sidelines of a cabinet meeting, Ihor Tenyukh said the deal had been struck with Russia's Black Sea fleet and the Russian defence ministry. "No measures will be taken against our military facilities in Crimea during that time," he said. "Our military sites are therefore proceeding with a replenishment of reserves."

The agreement has provided some respite for Ukraine's beleaguered troops, who have been trapped on their military bases and naval ships since Russian forces began occupying the peninsula on 27 February. They have been encircled ever since, in some cases without electricity. Residents have smuggled in food to them amid a standoff with the Russian military.

But there seems little doubt that Ukrainian forces will be evicted from Kremlin-controlled Crimea once the truce expires. Crimea's deputy prime minister, Rustam Temirgaliyev, said on Sunday that troops would be given safe passage and predicted that eastern Ukraine would be next to join Russia. "Donetsk, Lugansk, Kharkiv have the same situation as in Crimea – 75% of people want to join Russia in eastern Ukraine," he told journalists near the parliament building in Simferopol. There was further turmoil in Donetsk when pro-Russian protesters stormed the prosecutor's office and removed the Ukrainian flag from the roof, raising a Russian flag in its place. Riot police deployed to protect the building made little effort to stop the crowd, which later dispersed.

The government in Kiev has accused Moscow of deliberately stirring up tensions in the east by bringing in professional activists and provocateurs from across the border. In a series of ominous statements, Russia's foreign ministry has said it may be forced to act to "protect" ethnic Russians – an expression that appears to provide a rationale for future military incursions.

Self-defence volunteers line up outside the parliament in Kiev, Ukraine, after the referendum. Photograph: David Azia/AP

Putin spent Sunday evening at the closing ceremony of the Paralympic Games in Sochi but was keeping an eye on the Crimea results, his spokesman said. Earlier he had expressed concern about the escalation of tensions in the south and south-eastern regions of Ukraine, Reuters reported.

He blamed the febrile mood on "radical forces" acting with the "connivance of the current Kiev authorities". The Kremlin refuses to recognise Kiev's temporary government, that it says came to power on the back of a "fascist" coup.

Putin telephoned the German chancellor, Angela Merkel, on Sunday and told her that the referendum in Crimea complied with international law. The Russian leader had reportedly agreed that more observers from the Organisation for Security and Co-operation in Europe (OSCE) should be deployed in east Ukraine. Existing observers were refused entry to Crimea by pro-Russian checkpoint guards. On Saturday Russia vetoed a US-drafted motion in the UN security council in New York, which had declared the Crimea referendum invalid. China – a consistent ally of Moscow – abstained.

Ukraine's acting prime minister, Arseniy Yatsenyuk, has promised to take action against separatist "ringleaders" who, he said, had compromised his country's independence "under the cover of Russian troops". He said: "We will find all of them – if it takes one year, two years – and bring them to justice. The ground will burn beneath their feet."

The conflict spread from the ground to the internet, with several Nato websites targeted by hackers calling themselves CyberBerkut, after the Ukrainian riot police who were disbanded by the Kiev government. Crimean officials said their referendum website was also hacked.

Pro-unity rallies took place at the Maidan in Kiev on Sunday, the scene of Ukraine's revolution that led to President Viktor Yanukovych abandoning his office and fleeing to Russia last month. Some of those who attended were Crimeans who opposed secession and said they had left the peninsula in recent days amid threats and pressure.

Antonina Danchuk, 30, who lived in Simferopol until two years ago and studied Greek and English at its university, described the referendum as fake. "It's illegal," she said. "My Crimean friends who are there are afraid to go out and build their own Maidan. They're not voting. People with Russian passports are being allowed to vote."

Danchuk said she was not opposed to Russia, but to Putin and his expansionist policies. "I'm ethnic Russian. But I feel my nationality is Ukrainian. We've stayed in Ukraine for 22 years. We want Putin to leave us alone. We don't want Crimea to be a part of Russia."