In the lawsuit against the Justice Department, which was filed in federal court in the Western District of Washington, Microsoft argued it is unconstitutional to prevent the company from notifying its customers about these requests.
"Microsoft brings this case because its customers have a right to know when the government obtains a warrant to read their emails, and because Microsoft has a right to tell them," the tech giant says in its lawsuit.
The company said it is becoming routine for the government to issue orders requiring secrecy when it seeks information from email providers.
When asked for a comment on the lawsuit, a Justice Department spokesperson said, "We are reviewing the filing."
The suit focuses on how privacy protections should be applied to the way data is stored today, with much of it living on "the cloud" as opposed to personal computers or servers at customers’ homes.
"People do not give up their rights when they move their private information from physical storage to the cloud," the suit says. The government is exploiting the "transition to cloud computing as a means of expanding its power to conduct secret investigations," according to Microsoft.
They say the secrecy orders violate constitutional rights, which give individuals and businesses a right to know if the government is searching or seizing their property. Also, it narrows free speech when the government intervenes and does so for its own purposes, the company asserts in its suit.
Microsoft said it is worried about the practical ramifications of the Justice Department's current policy as more businesses and individuals store sensitive correspondence and other documents in cloud computing.
The tech company says there is an opportunity for the Justice Department to adopt a new policy that establishes reasonable limitations on the type of secrecy orders it uses. If the government doesn't act, Microsoft has asked for lawmakers on Capitol Hill to play a role in passing legislation that would protect people's rights and still provide flexibility for law enforcement.
ABC News' Mike Levine contributed to this report.