Yanukovych, appointed in August, has engaged in a power struggle with his long-standing rival Yushchenko for a dominant political role in Ukraine.
Constitutional changes, introduced at the height of the 2004 pro-Western Orange Revolution, made the prime minister nearly equal in power to the president.
In just two months, Yanukovych installed his allies to all key posts in financial, energy and economic sectors and poured cold water on Yushchenko's plans to win fast-track entry to NATO.
On Thursday, he took the battle for power to the regions.
A draft document, distributed at a government meeting, demanded the governors of the Poltava, Ternopil, Kharkiv, Kherson and Chernihiv regions -- all of them Yushchenko loyalists -- be sacked for "unsatisfactory solutions to problems that hamper social and economic development of the state."
Hiring and firing governors is the prerogative of the president.
"The political reasons behind such actions are obvious," Yushchenko's Our Ukraine party said. "We see such actions as another attempt of Prime Minister Viktor Yanukovych to overtake the president's powers," it added.