Google responded directly to Microsoft’s claims that Google had mislead its customers by claiming it has been certified under the Federal Information Security Management Act (FISMA).

Google’s director of security, Eran Feigenbaum, penned a company blog post on Wednesday to defend the company against Microsoft’s original claims. “Microsoft claims we filed a separate FISMA application for Google Apps for Government, then leaps to the conclusion that Google Apps for Government is not FISMA certified,” wrote Feigenbaum. “These allegations are false.”

Microsoft previously posted a stinging blog post earlier this week, publicly attacking Google. Microsoft’s Corporate Vice President & Deputy General Counsel David Howard, explained that the United States Department of Justice had rejected Google’s claim that Google Apps for Government, Google’s cloud-based suite for government customers, has been certified under the Federal Information Security Management Act (FISMA).

“So why did Google tell governments and the public that Google Apps for Government was FISMA certified even before it had applied for that certification? We’ll have to wait for Google to tell us what they were thinking,” said Howard in his original blog post.

Google claims Microsoft’s blog post was breathless. “We’ve been open and transparent with the government, and it’s irresponsible for Microsoft to suggest otherwise,” says Feigenbaum.

“Let’s look at the facts. We received FISMA authorization for Google Apps from the General Services Administration (GSA) in July 2010. Google Apps for Government is the same technology platform as Google Apps Premier Edition, not a separate system. It includes two added security enhancements exclusively for government customers: data location and segregation of government data. In consulting with GSA last year, it was determined that the name change and enhancements could be incorporated into our existing FISMA certification. In other words, Google Apps for Government would not require a separate application.”

WinRumors reached out to Microsoft for comment on Google’s blog post. Unsurprisingly a company spokesperson said “Microsoft does not have any comment.”