A statement on his website said Yanukovych left because of a respiratory illness and fever but did not indicate how long he would be absent, the New York Times reported.
Yanukovych went on sick leave before signing into law the repeal of draconian anti-demonstration and anti-free speech laws passed by lawmakers earlier this week. Without his signature, the repeal is basically meaningless, the Times said.
Ukrainian media reported two protesters were brought to a hospital with gunshot wounds Wednesday and one died. The death brings to four the number of protesters shot to death in recent days on Hrushevskovo Street, site of a standoff with police.
Earlier this week, Prime Minister Mykola Azarov resigned, triggering the resignation of the rest of Yanukovych's Cabinet. Opposition leaders and the government negotiated concessions in parliament and protesters vacated one occupied government building.
Negotiations began falling apart late Wednesday when the pro-government Party of Regions pushed through an amnesty law for protesters without support from opposition lawmakers, the Times said. The measure would require the prosecutor general to certify protesters vacated all occupied administrative buildings before amnesty would take effect and set a 15-day deadline to clear the buildings and would require police action after the deadline.
Opposition leader Vitali Klitschko of the Ukrainian Democratic Alliance for Reforms party said he and his supporters couldn't back the bill that essentially called for an end to the months-long protests without real change beyond freeing 218 activists the Interior Ministry said had been arrested, CNN reported.
"People took to the streets because they want to change the situation," Klitschko said. "A statement, 'We will free people, if they go home' is unacceptable. It cannot be understood."
"Today, the key issue is the confrontation between people and government," he said. "Withdrawal of charges and amnesty is not enough."
Protesters remained behind their makeshift barricades in Kiev's Independence Square and a road leading up to parliament, CNN said.
"I think the people should not leave the barricades," one Kiev resident told CNN. "Nothing is decided yet, let them decide -- now they just promise but don't make decisions. People are being tricked. They are tired of it."
One protester, Olga Lucuk-Visotska, told the BBC demonstrators considered those arrested as hostages, so the amnesty law isn't considered a compromise.
Leonid Kravchuk, Ukraine's first president after it became independent from what had been the Soviet Union, told parliament there was an urgency to resolve the crisis, CNN said.
"Let's be honest, the situation is dramatic. Both Ukraine and the world recognize the country is on the brink of civil war," Kravchuk said.
What sparked the protests was Yanukovych's decision in November not to sign political and trade agreements with the European Union after signaling he would. He then entered into agreements with Russia, which included a $15 billion deal for Russia to buy Ukrainian debt and cut the price of natural gas.
Moscow, meanwhile, signaled that it may hold back some of the promised bailout money until a new government is formed, the BBC said.
In Washington, congressional aides said financial sanctions against both officials and protest leaders were being prepared in case the violence worsens.