As rival neighbours east and west of the former Soviet republic said a power vacuum in Kiev must not lead to the country breaking apart, acting President Oleksander Turchinov said Ukraine's new leaders wanted relations with Russia on a "new, equal and good-neighbourly footing that recognises and takes into account Ukraine's European choice".
European Union foreign policy chief Catherine Ashton is travelling to Ukraine to discuss measures to shore up the ailing economy, which the finance ministry said needs £28 billion in foreign aid over the next two years.
Russian-backed Mr Yanukovich, 63, who fled Kiev by helicopter on Friday, is still at large after heading to his eastern power base, where he was prevented from flying out of the country, and then diverting south to the Crimea, acting interior minister Arsen Avakov said.
Mr Avakov added: "An official case for the mass murder of peaceful citizens has been opened. Yanukovich and other people responsible for this have been declared wanted."
Mr Yanukovich had left a private residence in Balaclava, in the Russian-speaking Crimea, for an unknown destination by car with one of his aides and a handful of security guards, Mr Avakov said.
It was an ignominious political end for the president who has been publicly deserted by some of his closest erstwhile allies, stripped of his luxury residence outside Kiev and has witnessed the return of his arch rival Yulia Tymoshenko.
Russian Prime Minister Dmitry Medvedev said Moscow had grave doubts about the legitimacy of those in power in Ukraine following Mr Yanukovich's removal, saying their recognition by some states was an "aberration".
Mr Medvedev said: "We do not understand what is going on there. There is a real threat to our interests and to the lives of our citizens. There are big doubts about the legitimacy of a whole series of organs of power that are now functioning there."
Russia recalled its ambassador from Kiev on Sunday, accusing the Ukrainian opposition of having torn up a transition agreement with the president it supported.
On Independence Square in central Kiev, cradle of the uprising, barricades of old furniture and car tyres remained in place, with smoke rising from camp fires among tents occupied by diehard protesters vowing to stay until elections in May.
The mood among the few hundred in the square was a mixture of fatigue, sorrow for the 82 people killed last week, and a sense of victory after three months of protests.
Protester Grigoriy Kuznetsov, 53, who was dressed in black combat fatigues, said: "Now is not the time for celebrating. We are still at war. We will stay here as long as we have to."
Mr Turchinov, the parliament's speaker, was named interim head of state on Sunday. An ally of the ousted leader's rival, Yulia Tymoshenko, he aims to swear in a government by today that can run things until a presidential election on May 25.
With battle-hardened, pro- Western protesters in control of Kiev and determined to hold their former leaders to account, lawmakers rushed through decisions to cement their power, show their rejection of rampant corruption and bring to justice officials who ordered police to fire on Independence Square.
Whoever takes charge faces a huge challenge to satisfy popular expectations and will find an economy in deep crisis and which faces state debt payments of around £3.6bn in the remainder of this year.
Scuffles in Crimea and some eastern cities between supporters of the new order in Kiev and those anxious to stay close to Moscow revived fears of separatism. A week ago those concerns were focused on the West, where Ukrainian nationalists had disowned Yanukovich and proclaimed self-rule.