Is it possible government agencies are unfairly favoring Microsoft? According to a Reuters report, Google thinks this may be the case as the Internet giant did not have the opportunity to bid on the largest federal government cloud computing struck to date.

On Wednesday, the United States Department of Agriculture (USDA) announced that it was moving 12,000 of its employees onto e-mail, Web conferencing and messaging systems provided via the Internet by Microsoft.

According to the USDA, this move to the cloud is a part of a deal the agency signed with Dell in may to provide online services from Microsoft. The agency has been working with the two companies for the past six months on the project, which is worth $27 million over three years and is expected to save the USDA about $6 million per year.

This move is the largest to date of any kind like it completed by a federal agency. It is also the first by a cabinet-level department in the growing area hotly contested by Microsoft and competitor Google. One point of contention is that while Google’s offering may be less known, they are less expensive.

The area of procurement of technology by U.S. government agencies has been under the microscope lately. Just last month, Google sued the U.S. government for excluding its products from consideration for a 5-year contract worth $59 million to upgrade the e-mail system for the Interior Department.

As the incumbent provider, Microsoft tends to win the most government technology contracts in this area. For its part, Google did just recently claim some high-profile contracts to provide a version of its online Google Apps service to the U.S. General Services Administration, the state of Wyoming and the city of Los Angeles.

Google has claimed that its services can deliver better cost savings than Microsoft solutions. The company also argues that its solutions are lower in price overall and in a bidding situation, would have won the contract.

A spokesman for the company noted that Google was not given the opportunity to bid for the USDA business. The company highlighted that when there is a full and open competition, customers have chosen Google Apps and taxpayers save millions.

The agency reportedly looked at Google offerings informally two years ago when it had decided to overhaul and consolidate its disparate e-mail systems. The agency preferred Microsoft as it already had large investments in the company’s e-mail systems and SharePoint Web collaboration tool.

While the USDA did consider other options, Microsoft was determined to be the best solution.