In a blog post on Wednesday, the company's corporate vice-president and general counsel, Dev Stahlkopf, said the suit, filed in September last year, had been unsealed recently.
He said the challenge to the secrecy order had been made in Brooklyn, New York, in connection with a federal national security investigation. The warrant is known as "sneak and peek" and does not require the subject of a federal inquiry to be notified that the government wants access to their data.
"The secrecy order prevents Microsoft from notifying our enterprise customer that we received a warrant seeking its data," Stahlkopf said.
A lower court had turned down Microsoft's order and Stahlkopf said the company had challenged it, and would pursue an appeal to the appellate court if needed.
"When a law enforcement agency presents Microsoft with a legally valid warrant, court order or subpoena requesting data that belongs to one of our enterprise customers, we seek to redirect that request to the customer, he wrote.
"And in the vast majority of cases, that is exactly what happens. There are times, however, when the government comes to us for data and prevents us from telling our enterprise customers that it is seeking their data.
"We agree that there are some limited circumstances in which law enforcement must be able to operate in secret to prevent crime and terrorism and keep people safe.
"And while we agree that secrecy orders that prevent us from notifying our customers may be appropriate in those limited circumstances, we also believe there are times when those orders go too far. In those cases, we will litigate to protect our customers’ rights."
Microsoft has fought the US Government in the past, when Washington sought to access data stored by one of its customers in Ireland in 2013. The protracted case ended with the passage of the CLOUD (Clarifying Lawful Overseas Use of Data) Act that changed US law so that law-enforcement warrants apply to data stored anywhere by US-based tech firms.