SAN FRANCISCO –Google Inc. (GOOG) is suing the U.S. Department of the Interior, alleging the agency inappropriately wrote procurement requirements for a messaging contract to favor Microsoft Corp. (MSFT) over its own Google Apps.

The suit, filed Friday in the U.S. Court of Federal Claims, claims the agency’s request for quotations for an e-mail and collaboration product was written to exclude Google by specifically stating the solution had to be part of the Microsoft Business Productivity Online Suite.

The DOI’s decision to only consider Microsoft’s productivity suite is “unduly restrictive of competition” and violates the Competition in Contracting Act, said Google in a claim filed with its government-reselling partner Onix Networking Corp.

The U.S agency is looking for a single hosted email and collaboration solution to replace the 13 messaging platforms currently in place for its 88,000 users. The contract is estimated to be worth $59 million over five years.

Google’s suit seeks to block the DOI from proceeding with requests for bids on the contract without first conducting a competitive procurement process.

Google’s lawsuit turns the table on the U.S. government, which has stepped up its scrutiny and probes of the Mountain View, Calif.-based search giant’s acquisitions and privacy practices in recent months.

The lawsuit is also part of the company’s ongoing battle with Redmond, Wash.-based Microsoft, in which Google has been pushing its Google Apps online productivity services as a alternative to Microsoft’s packaged Office software.

The two companies have faced off over many government contracts for email and other productivity software. Google Apps, the company’s “cloud computing” service costs $50 per user per year, while Microsoft recently launched its own cloud-computing Office service for as little as $2 per user per month.

“Google rarely goes on the offensive in court,” said Eric Goldman, professor at Santa Clara University School of Law. “It’s suing the Department of the Interior as a proxy in its battle against Microsoft.”

According to the complaint, DOI officials told Google they were committed to an open competition for the contract even though the department had “standardized” on Microsoft technology.

But the department also cited concerns about whether Google could comply with the agency’s security needs, ultimately concluding that Microsoft was the only vendor that met all of the department’s requirements, according to the lawsuit.

James Kim, an attorney at McDermott Will & Emory LLP, said Google faces a relatively high bar to prove to the court that the DOI acted inappropriately. The agency must only provide a “rational explanation” as to why it wrote the RFQ in such a manner, such as cost considerations, compatibility, or the ease of training users, he said.

Kim added that while bid protests were not uncommon, they are “generally the line of last resort.”

The DOI, Google and Microsoft were not immediately available for comment.