Microsoft is calling Google’s security claims into question with accusations that it misled the U.S. government.

According to a blog post from Microsoft Corporate Vice President & Deputy General Counsel David Howard, a Justice Department brief found that Google does not have Federal Information Security Management Act (FISMA) certification for its Google Apps for Government suite for government customers. Google’s site clearly states that the suite is FISMA certified.

The Justice Department brief is related to case that Google brought against the government saying that the Department of Interior’s decision to go with Microsoft’s cloud-based e-mail was not competitive.

“When it comes to security, the facts matter,” Howard wrote in the post.

In response to Microsoft and the Justice Department, Google defended its statement saying it had FISMA certification. David Mihalchik of Google Enterprise issued the following statement:

This case is about the Department of Interior limiting its proposal to one product that isn’t even FISMA certified, so this question is unrelated to our request that DOI allow for a true competition when selecting its technology providers.

Even so, we did not mislead the court or our customers.  Google Apps received a FISMA security authorization from the General Services Administration in July 2010. Google Apps for Government is the same system with enhanced security controls that go beyond FISMA requirements. As planned we're working with GSA to continuously update our documentation with these and other additional enhancements.

The city of Los Angeles has been transitioning to Google’s suite for some of its 30,000 city employees, the Los Angeles Times reported.

According to consumer advocacy group Consumer Watchdog, two L.A. city council committes have held a unrelated hearings questioning whether Google’s security requirements are tough enough for the city’s police department.