The moves pose an immediate challenge to Ukraine's new authorities as they seek to set up an interim government for the country, whose population is divided in loyalties between Russia and the West.
Ukraine's new prime minister said the country's future lies in the European Union but with friendly relations with Russia. Moscow, meanwhile, has launched a major military exercise involving 150,000 troops and put fighter jets on patrol along the border.
Respected Russian news organization RBK reported that Viktor Yanukovych, who was driven out of Kiev by a three-month protest movement against his government, was staying in a Kremlin retreat just outside Moscow after first staying at a hotel.
"I have to ask Russia to ensure my personal safety from extremists," the fugitive leader said in a statement carried by Russian news agencies on Thursday. He said he still considers himself president and sees the new Ukrainian authorities as illegitimate.
The same agencies then quoted an unnamed Russian official saying that Yanukovych's request for protection "was satisfied on the territory of Russia."
Yanukovych will reportedly hold a news conference Friday in the southern Russian city of Rostov-on-Don. Russian officials, including President Vladimir Putin's spokesman, said they had no information about Yanukovych's reported arrival in Moscow.
Yanukovych's decision to ditch closer ties to the European Union and turn to Moscow instead sparked weeks of protests in Kiev. He fled after riot police attacked protesters in Kiev's central square, killing more than 80 people, and European and Russian officials intervened. He hasn't been seen publicly since Saturday, when he said he remained the legitimately elected president — a position that has been backed by Russia.
In Kiev, lawmakers chose Arseniy Yatsenyuk as the new prime minister. He will face the hugely complicated task of restoring stability in a country that is not only deeply divided politically but on the verge of financial collapse. The 39-year-old served as economy minister, foreign minister and parliamentary speaker before Yanukovych took office in 2010, and is widely viewed as a technocratic reformer who enjoys the support of the U.S.
Shortly before the lawmakers chose him as the leader of the new Cabinet, Yatsenyuk said Ukraine doesn't want a fight with Russia, but insisted the country wouldn't accept the secession of the southern Crimea region.
He said Crimea "has been and will be a part of Ukraine."
The Black Sea peninsula, where a majority of residents are ethnic Russians and where Russia maintains a naval base, has become the latest flashpoint in Ukraine's political crisis. A day after pro- and anti-Russian rallies in the regional capital of Simferopol, witnesses said gunmen wearing unmarked camouflage uniforms and carrying rocket-propelled grenades, sniper rifles and other weapons seized local government buildings and raised the Russian flag over the regional parliament.
They didn't immediately voice any demands and threw a flash grenade in response to a journalist's questions. They wore black and orange ribbons, a Russian symbol of the victory in World War II, and put up a sign reading "Crimea is Russia."
Later in the day, hundreds of pro-Russian protesters gathered outside the parliament, waving Russian flags and signs calling for Crimea to join Russia. Oleg Slusarenko, a protest organizer, announced to the crowd that deputies had voted to hold a referendum on expanding Crimea's autonomy on May 25.
Russian news agencies reported that the Crimean legislature had held an emergency session — despite the occupation of the building — and removed the local governor, replacing him with Sergei Aksyonov, the head of Russian Unity, the main pro-Russian party on the peninsula.
It wasn't immediately clear what effect the decisions would have in practice.
Phone calls to the Crimean legislature rang unanswered, and its website was down.
Oleksandr Turchynov, who stepped in as Ukraine's acting president after Yanukovych's flight, denounced the gunmen who seized control of the government buildings in Crimea and warned that any move by Russian troops off of their base in Crimea "will be considered a military aggression."
"I have given orders to the military to use all methods necessary to protect the citizens, punish the criminals, and to free the buildings," he said.
Ukraine's ambassador to NATO, Ihor Dolhov, told The Associated Press in Brussels that Turchynov was supposed to go to Crimea later Thursday. Russian news agency Interfax later reported that he wasn't going.
In another sign of the ongoing tensions in Crimea, an AP freelancer saw a convoy of seven armored personnel carriers on a road near the village of Ukromnoye, about 10 kilometers (6 miles) from Simferopol. The soldiers manning the APCs didn't answer questions, and the APCs turned away and headed away from Simferopol. Their nationality wasn't immediately clear.
In a clear warning to Ukraine, Putin on Wednesday ordered major exercises involving most of the military units in western Russia. As part of the exercises, fighter jets were put on combat alert Thursday and were patrolling the border, Russia's Defense Ministry said in a statement. It didn't specify the areas where patrol missions were being conducted. The military also announced measures to tighten security at the headquarters of Russia's Black Sea Fleet on the Crimean peninsula in southeastern Ukraine.
In Brussels, U.S. Defense Secretary Chuck Hagel urged Russia not to take any action on Ukraine that might boost tensions. After a NATO defense minister meeting, he told reporters: "These are times for cool, wise leadership on Russia's side and everyone's side."
NATO Secretary-General Anders Fogh Rasmussen said Russian authorities had informed the U.S. alliance of the military exercises, and "made it clear" they have nothing to do with Ukraine.
"Having said that, obviously it doesn't make things easier that there is a coincidence between the timing of this exercise and the ongoing events in Ukraine," Rasmussen said.
Russia's Foreign Ministry voiced concern about the Russian-speaking population in Ukraine and vowed to protect their interests. Russia has accused Ukraine's interim leaders of failing to control radicals who threaten the Russia-speaking population in Ukraine's east and south, which includes the Crimean Peninsula.
In Simferopol, a pro-Russian activist who identified himself only as Maxim, said he and other activists had camped overnight outside the local parliament when 50-60 heavily armed men wearing flak jackets and carrying rocket-propelled grenade launchers and sniper rifles took over the building.
"Our activists were sitting there all night calmly, building the barricades," he said. "At 5 o'clock unknown men turned up and went to the building. They got into the courtyard and put everyone on the ground.
"They were asking who we were. When we said we stand for the Russian language and Russia, they said: 'Don't be afraid. We're with you.' Then they began to storm the building bringing down the doors," he said. "They didn't look like volunteers or amateurs; they were professionals. This was clearly a well-organized operation."
"Who are they?" he added. "Nobody knows."
In Moscow, Russia's Foreign Ministry said that Russia was abiding by an agreement with Ukraine that sharply restricts troop movements, and added that some unspecified movements of troops had taken place, but it didn't violate that deal, the Interfax news agency reported.
In a statement, the local government said Crimean Prime Minister Anatoly Mogilyev had tried to negotiate with the gunmen but was told "they were not authorized to negotiate and present demands."
Meanwhile, Ukraine's currency, the hryvnia, dropped further to a new record low of 11.25 to the U.S. dollar, a sign of the country's financial distress.
One of the new government's first tasks will be to seek rescue loans from the European Union and the International Monetary Fund. The finance ministry has pegged the country's needs at $35 billion dollars for this year and next to pay salaries and debts and cover the large budget deficit.
It will also have to deal with the angry street protesters who set up camp on Kiev's Independence Square, also known as Maidan, during the uprising against Yanukovych. Many of them worry that the new government will not address their grievances, including the endemic corruption in Ukraine's political system.
Hundreds of protesters from the Maidan movement gathered outside Parliament on Thursday, placing car tires and unlit Molotov cocktails at the entrance as if to remind lawmakers that the street revolt could easily re-ignite.