"There probably are some cases where (the government) should be able to go in covertly and get information about a company’s email," Gates said at a Reuters Newsmaker event in Washington.
"But the position Microsoft is taking in this suit is that it should be extraordinary and it shouldn’t be a matter of course that there is a gag order automatically put in,” he said in an interview with Reuters Editor-in-Chief Stephen Adler.
The lawsuit, filed last week in federal court in Microsoft's home town of Seattle, argues that the government is violating the US Constitution by preventing Microsoft from notifying thousands of customers about government requests for their emails and other documents, sometimes indefinitely.
The move comes as rival Apple Inc is locked in a showdown with the US government over access to an iPhone belonging to one of the killers in the December shooting in San Bernardino, California.
Gates said more collaboration between law enforcement and privacy advocates would help determine which “legislative framework ... strikes the perfect balance” on government access to private data.
“I don’t think there are any absolutists who think the government should be able to get everything or the government should be able to get nothing,” Gates, 60, said.
The man who co-founded Microsoft in 1975 and is still held in reverence by the technology world made waves in February when he appeared to distance himself from Apple in its legal fight with the US Federal Bureau of Investigation, but later clarified his comments and said that headlines suggesting he supported the FBI’s position were inaccurate.
The foundation, where Gates works day to day, has focused attention in recent months on the Zika outbreak, which has been linked to thousands of suspected cases of microcephaly, a rare birth defect, in Brazil and is affecting large parts of Latin America and the Caribbean.
The World Health Organisation declared the outbreak an international health emergency on Feb 1.
Gates said the foundation would be contributing funds to aid in the Zika fight, but did not say how much.
Private sector and governments need to work together to quickly roll out products to combat Zika and other mosquito-borne diseases, Gates said.
"Zika is a tough one," he said. "There are potential solutions. They won't come soon enough to avoid some problems in the entire hemisphere."