Fears of a major regional conflict in Crimea pitting Russia against the west intensified on Thursday after pro-Russian gunmen seized the regional government and parliament building in a well co-ordinated military operation, while similar groups were on Friday morning controlling access to the airports of Simferopol and Sevastopol.

Early on Friday morning about 50 armed gunman reportedly marched into Simferopol's airport after arriving in Kamaz trucks. They first cordoned off the domestic terminal and then moving on to other areas. Russia Today described them as similarly dressed and equipped to the "local ethnic Russian 'self-defence squads'" that seized the parliament and government buildings.

Witnesses said the men at the airport were bearing Russian navy flags. The AFP news agency said the airport was operating as Friday dawned, with passengers checking in for flights. The Associated Press said dozens of the armed men continued to patrol the airport and they refused to speak to media. AFP said representatives from the new leadership in Kiev had been due to arrive at the airport on Friday.

In Sevastopol armed men were reported to have set up a perimeter around the city's combined military-civilian airport, known as Belbek, on Friday morning. The Interfax news agency described them as Russian servicemen who said they had gone to Belbek to stop "fighters" flying in.

A gunman outside Simferopol airport in Crimea. Photograph: David Mdzinarishvili/Reuters

On Thursday morning in Simferopol men dressed in fatigues stormed Crimea's administration, hoisting a Russian flag above the parliament building. About 120 men were holed up inside armed with heavy weapons including rocket-propelled grenades and sniper rifles, witnesses said.

With gunmen controlling the building, Crimea's parliament voted to hold a referendum on the region's status on 25 May, the same day Ukraine goes to the polls in presidential elections. It also voted to sack the region's cabinet. The move puts the predominantly ethnic-Russian region on a collision course with Kiev's interim government and will fuel concern Ukraine is sliding inexorably towards break-up.

It was unclear whether the gunmen were undercover Russian soldiers or members of a pro-Russian self-defence militia formed in response to Ukraine's revolution, which has included radical nationalist groups. The former head of the Crimean parliament, Serhiy Kunitsyn, described the men as professionally trained and armed with enough weaponry to defend the complex for a month.

Late on Thursday the US vice-president, Joe Biden, spoke with Ukraine's interim prime minister, Arseniy Yatsenyuk. Biden promised Ukraine's new leadership the full support of the US, a White House statement said.

Russia's ousted ally Viktor Yanukovych, the former Ukraine president, who fled Kiev last week after his troops shot dead more than 80 people, resurfaced on Thursday to insist he was still the country's legitimate leader – excoriating Ukraine's new leadership as he did so.

That government confirmed 39-year-old former opposition leader Arseniy Yatsenyuk as acting prime minister, and gave two of the former regime's most prominent victims places in the new administration. Tetiana Chornovol, an investigative journalist beaten up by thugs, heads a new anti-corruption office. Activist Dmytro Bulatov, who was kidnapped and had part of his ear cut off, becomes Ukraine's youth minister.

Ukraine's acting president, Oleksandr Turchynov, who has been in the job since Yanukovych fled the country, warned Russia not to intervene in the crisis by moving troops. The Kremlin's Black Sea fleet is based near Simferopol in the port of Sevastopol. Turchynov said: "I am appealing to the military leadership of the Russian Black Sea fleet. Any military movements, the more so if they are with weapons, beyond the boundaries of this territory [the base] will be seen by us as military aggression." Ukraine's foreign ministry also summoned Russia's acting envoy in Kiev for consultations.

The White House said it was closely watching Russian's military manoeuvres, ordered by Vladimir Putin next to Ukraine's border. Putin also put fighter jets on a state of high alert.

The US defence secretary, Chuck Hagel, called on the Kremlin to show restraint and reaffirmed Washington's commitment to Ukraine's territorial integrity and sovereignty.

After meeting Angela Merkel, David Cameron said he and the German chancellor were particularly concerned. Nato's secretary general, Anders Fogh Rasmussen, urged Russia not to do anything that would escalate tension or create misunderstanding.

Poland's foreign minister, Radoslaw Sikorski, described the seizure of government buildings in the Crimea a "very dangerous game". He told a news conference: "This is a drastic step, and I'm warning those who did this and those who allowed them to do this, because this is how regional conflicts begin."

Hours after the parliament building was seized, Yanukovych revealed he was in Russia and had sought protection from Putin. He said he would hold a press conference on Friday in Rostov-on-Don, close to Ukraine's border and his home city of Donetsk.

His unusual choice of a provincial press conference venue suggests he still nurtures hopes of a return to power, possibly as the leader of a breakaway Russian-backed enclave encompassing Crimea and eastern Ukraine.

Yanukovych appeared to give approval to secessionist pro-Russian forces in Crimea, and said an "orgy of extremism" had swept the country. "Now it is becoming clear that the people in south-eastern Ukraine and in Crimea do not accept the power vacuum and complete lawlessness in the country," he said.

In Kiev, members of Ukraine's new government hinted that the country would sign an association agreement with the EU next month. It was Yanukovych's decision in December to dump the agreement – and instead accept a bailout from Russia – that prompted the street demonstrations that eventually led to his overthrow. Ukrainian officials branded the referendum decision by Crimea's parliament as unconstitutional.

Earlier in Simferopol, the gunmen barricaded doors into the parliament building with wooden crates. Police sealed off the area on Thursday, as a crowd supportive of the seizure gathered outside. Two people died and 35 were injured during clashes outside the building on Wednesday between pro-Russian demonstrators and Muslim Tatars. About half of Crimea's 2 million population are ethnic Russians. The Tatars – the peninsula's original Turkic-speaking Muslim inhabitants – are 300,000 strong and support the authorities in Kiev.

Witnesses described the moment when the armed men turned up. "We were building barricades in the night to protect parliament. Then this young Russian guy came up with a pistol … we all lay down, some more ran up, there was some shooting and around 50 went in through the window," Leonid Khazanov, an ethnic Russian, told Reuters.

Khazanov added: "They're still there … Then the police came, they seemed scared. I asked them [the armed men] what they wanted, and they said: 'To make our own decisions, not to have Kiev telling us what to do'."

The former head of the central executive body of Crimean Tatars, Mustafa Jemilev, said the situation was extremely worrying. He suggested the gunmen had arrived from Sevastopol, where the Russian fleet is based. "The people in camouflage and without any distinctive signs came by buses from the Sevastopol side. There are reports of movement of armed vehicles of the Russian fleet in different directions. We also got signs that in many hotels there are Russian soldiers wearing civilian clothes. The Russian general consul office says they have nothing to do with these events. But they would hardly tell the truth."

Jemilev speculated that the gunmen could be Russian soldiers or members of Berkut, the now-disbanded riot police unit deployed against opposition protesters in Kiev. Lifenews.ru, a pro-Kremlin Russian website with links to Russia's spy agencies, however, said they were veterans from the army and police. According to US diplomatic cables leaked in 2010 by Wikileaks, Russia's military intelligence wing – the GRU – is highly active in Crimea.

About 100 police had gathered in front of the parliament building on Thursday. A similar number of people carrying Russian flags later marched up to the building chanting "Russia, Russia" and holding a sign calling for a Crimean referendum.

Many wore orange-and-black striped ribbons that symbolise support for Russia. One of them, Alexei, 30, said: "We have our own constitution, Crimea is autonomous. The government in Kiev are fascists, and what they're doing is illegal … We need to show our support for the guys inside [parliament]. Power should be ours."

"Yesterday Russian people were attacked and murdered by Tatar extremists. We will not allow this fascism from Kiev to happen here," said 43-year-old construction worker, Spartak. "Crimea wants independence and we want parliament to hold a referendum on this. We have been hijacked."

Policemen informed passersby that Karl Marx Street was closed due to the presence of snipers in the areas. Nearby shops and businesses have closed and pulled down their shutters.

The acting interior minister, Arsen Avakov, who said the attackers had automatic weapons and machine guns, urged calm. He said on Facebook: "Provocateurs are on the march. It is the time for cool heads."

Turchynov, speaking to the parliament in Kiev, described the attackers as "criminals in military fatigues with automatic weapons".

He also called on Moscow not to violate the terms of an agreement that gives the Russian Black Sea fleet basing rights at Sevastopol until 2042.