Schmidt questions openness in deal that has not yet taken off.
Google, the world's leading search engine, said on Monday it was concerned about the free flow of information on the Internet if Microsoft were to succeed in acquiring Yahoo.
Last month, Microsoft proposed buying Yahoo in a deal originally worth $44.6 billion, but Yahoo's board has rejected the offer, saying it was too low.
"We would be concerned by any kind of acquisition of Yahoo by Microsoft," CEO Eric Schmidt told reporters.
"We would hope that anything they did would be consistent with the openness of the Internet, but I doubt it would be."
Schmidt pointed to Microsoft's past history and "the things that it has done that have been so difficult for everyone," but he did not elaborate.
Last year, a European court upheld a landmark 2004 decision that Microsoft abused the near-monopoly power of its Windows operating system to damage competitors, along with a 497 million euro ($695 million) fine.
"We are concerned that there are things Microsoft could do that would be bad for the Internet," said Schmidt.
Microsoft CEO Steve Ballmer pledged earlier this month that his company would gain market share against Google in online advertising and Web searching, even if led to his "last breath" at the company.
In a Reuters poll of financial analysts, the overwhelming majority said they believed Microsoft would eventually succeed in buying Yahoo, but many said they felt it may not be the best use of its ample cash reserves.