Yanukovych himself has reportedly fled to the Black Sea peninsula of Crimea, a pro-Russian area in Ukraine.
Calls are mounting in Ukraine to put Yanukovych on trial, after a tumultuous presidency in which he amassed powers, enriched his allies and family and cracked down on protesters. Anger boiled over last week after government snipers killed scores of protesters in the bloodiest violence in Ukraine's post-Soviet history.
The turmoil has turned this strategically located country of 46 million inside out over the past few days. The parliament speaker is now nominally in charge of a country whose ailing economy is on the brink of default and whose loyalties are sharply torn between Europe and longtime ruler Russia.
Russia and the European Union appeared to be taking opposing sides in Ukraine's new political landscape.
Russian Prime Minister Dmitry Medvedev questioned the legitimacy of the new Ukrainian authorities on Monday. According to Russian news agencies, he said the acting authorities have come to power as a result of an "armed mutiny," so their legitimacy is causing "big doubts."
In Brussels, European Commission spokesman Olivier Bailly referred to parliament speaker Oleksandr Turchinov as the "interim president" and said Turchinov will meet with Monday visiting EU foreign policy chief Catherine Ashton in Kiev.
Turchinov said he hopes to form a new coalition government by Tuesday.
Ukraine's acting interior minister, Arsen Avakhov, said on his official Facebook page that a warrant has been issued for the arrest of Yanukovych and several other officials for the "mass killing of civilians."
At least 82 people, primarily protesters, were killed in clashes in Kiev last week.
Yanukovych set off a wave of protests by shelving an agreement with the European Union in November and turning instead for a $15 billion bailout loan from Russia. Within weeks, the protests expanded to include outrage over corruption and human rights abuses, leading to calls for Yanukovych's resignation.
After signing an agreement Friday with the opposition to form a unity government, Yanukovych fled Kiev for his pro-Russian power base in eastern Ukraine. Avakhov said he tried to fly out of Donetsk but was stopped then went to Crimea on Sunday.
Yanukovych then freed his official security detail and drove off to an unknown location, turning off all forms of communication, Avakhov said.
"Yanukovych has disappeared," he said.
Security has been tightened across Ukraine's borders, the Interfax news agency quoted the State Border Guard service as saying.
Avakhov published a letter that he said was from Yanukovych, dated Monday, in which he gave up his security guard. Yanukovych's aides and spokespeople could not be reached Monday to verify the reported letter — they have been rapidly distancing themselves from him as his hold on power disintegrates.
Activist Valeri Kazachenko said Yanukovych must be arrested and brought to Kiev's main square for trial.
"He must answer for all the crimes he has committed against Ukraine and its people," he said, as thousands continued to flock to the area to light candles and lay flowers where dozens were shot dead during clashes with police last week. "Yanukovych must be tried by the court of the people right here in the square."
Tensions have been mounting in Crimea in southern Ukraine. Russia maintains a large naval base in Sevastopol that has strained relations between the countries for two decades.
Pro-Russian protesters gathered in front of city hall in the port of Sevastopol on Monday chanting "Russia! Russia!"
"Extremists have seized power in Kiev and we must defend Crimea. Russia must help us with that," said Anataly Mareta, head of a Cossack militia in Sevastopol.
The head of the city administration in Sevastopol quit Monday amid the turmoil, and protesters replaced a Ukrainian flag near the city hall building with a Russian flag.
Russian President Vladimir Putin's position on the turmoil in Ukraine will be crucial to the future of Crimea and to Ukraine. Putin spoke with German Chancellor Angela Merkel by telephone Sunday and the German government said the two agreed that Ukraine's "territorial integrity must be respected."
On Monday, German government spokesman Steffan Seibert told reporters that Ukraine's new leaders should consider the interests of the south and east — the pro-Russian sections of Ukraine — in the composition of a new government. He also said the offer of an association agreement with the EU is still on the table.
As president, Yanukovych moved quickly to consolidate power and wealth, curb free speech and oversee the imprisonment of his top political rival, former Prime Minister Yulia Tymoshenko. But as protesters took control of the capital over the weekend, many allies turned against him.
Yet Yanukovych has proved politically resilient in the past. In Ukraine's 2004 Orange Revolution, when protesters pressed for democratic reforms, his fraud-ridden victory in presidential elections was overturned. He soon came back as prime minister and then was elected president in 2010, riding on a wave of popular disappointment in the squabbling Orange team.
But Yanukovych's archrival Tymoshenko, the blond-braided heroine of the 2004 Orange Revolution, is back on the political scene after having been freed from prison.
The current protest movement in Ukraine has been in large part a fight for the country's economic future — for better jobs and prosperity.
Ukraine has a large potential consumer market, an educated workforce, a significant industrial base and good natural resources, in particular rich farmland. Yet its economy is in tatters.
Ukraine has struggled with corruption, bad government and short-sighted reliance on cheap gas from Russia. Political unrest has pushed up the deficit, sent the currency skidding and may have pushed the economy back into a recession.
"The state treasury has been torn apart, the country has been brought to bankruptcy," Arseniy Yatsenyuk, a protest leader and prominent lawmaker whose name is being floated as a possibility for prime minister, said in parliament Monday.
Ukraine's acting finance minister said Monday that the country needs $35 billion (25.5 billion euros) to finance government needs this year and next and expressed hope that Europe or the United States would help. The minister, Yuri Kolobov, said Ukraine hopes for an emergency loan within the next two weeks and called for an international donors conference to discuss aid to Ukraine.