BALAKLAVA, Ukraine—Ousted Ukrainian President Viktor Yanukovych was on the run Monday from a new government, which issued an arrest warrant for him on allegations of ordering the "mass murder" of protesters on the streets of Kiev last week.

Opposition parties—who over the weekend gained control of parliament and voted to dismiss Mr. Yanukovych—now want the toppled leader held accountable for deadly clashes in Kiev that left more than 80 protesters and police dead. Ukraine's acting interior minister, Arsen Avakov, used his Facebook page Monday to deem Mr. Yanukovych an officially wanted man.

"As of this morning, a criminal case has been opened based on the mass murder of civilians," Mr. Avakov wrote in his post. "Yanukovych and some other officials have been put on the wanted persons list."

The transformation of Mr. Yanukovych from the country's elected leader to a hounded runaway has been stunning in its speed. Within four days, he has gone from an embattled Ukrainian leader negotiating with foreign diplomats to a full-fledged man on the run, the subject of swirling rumors about fanciful escape attempts via helicopter, private jet and boat.

The 63-year-old deposed president dropped out of sight after he was last publicly seen Saturday in a video, in which he denounced his removal from power as a coup and declared himself Ukraine's legitimately elected president.