The referendums planned to be held in several cities in eastern Ukraine are illegal, Xinhua quoted a joint statement of the two leaders as saying as Hollande visited Germany's port city of Stralsund.
Merkel said Germany and France saw the vote, arranged to take place in eastern Ukraine Sunday, as illegal.
Both countries said they would support holding a free and fair presidential election across the whole of Ukraine May 25.
Hollande said he and Merkel condemned the vote in eastern Ukraine during their talks. "The referendum on Sunday has no significance for us."