The study seems to make some large assumptions about how much money federal agencies can save, said Susie Adams, CTO of Microsoft Federal. The study "really tries to simplify a very complex problem," she said.

Microsoft agrees that agencies can save money using cloud computing and virtualization, but open-source software is "just another business model," Adams said. Agencies should explore the entire cost before making a decision about open-source software, she added.

"In today's world, especially in the government, we're really looking at a mixed-source environment," Adams said. "We believe that what we should be doing is creating software that's more interoperable with this mixed environment. We're committed to that."

Critics of the report may be able to quibble with the numbers, but the big message is that federal agencies should be looking at new ways to save money with IT investments, said Peter Tseronis, deputy associate chief information officer for the U.S. Department of Energy. The study, plus ongoing conversations about federal IT spending at MeriTalk.com, highlight the need for federal agencies to look at new ways of doing business and to think strategically about long-term IT investments, he said.

"The infrastructure itself needs to be sound -- it needs to be stable," Tseronis said. "If you don't have a solid base, it's not going to matter what's on your desktop."