After many years of legal uncertainty, a federal appeals court has finally declared that emails have the same Fourth Amendment protections as regular mail and telephone calls.

“Given the fundamental similarities between email and traditional forms of communication, it would defy common sense to afford emails lesser Fourth Amendment protection,” the Sixth Circuit Court of Appeals ruled (PDF).

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If the ruling is not overturned by the Supreme Court, it will put an end to the practice of law enforcement agents using court orders, rather than warrants, to gain access to emails. Court orders require a much lower standard than warrants.

Kevin Bankston of the digital rights group EFF told Wired.com he expects Internet service providers will comply with the ruling, meaning they will start requesting warrants when law enforcement requests access to emails.

Privacy advocates say law enforcement has been using a loophole in the 1986 Stored Communications Act to get emails without a warrant. Under that law, information stored on servers is subject only to a court order.

As Wired notes, the law was written at a time when emails — then still a novelty — weren’t stored on remote servers. But today’s email services, such as Hotmail and Gmail, use servers to store all emails, giving law enforcement warrantless access.

A group of businesses, including Microsoft, Google and AOL, have been lobbying the US to update its laws so that all emails require a warrant.

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At issue in the Sixth Circuit’s ruling was the criminal case of Steven Warshak, founder of the company that sells Enzyte “male enhancement” pills. Warshak was given a 25-year sentence in 2008 after being convicted of 93 counts of fraud, conspiracy and money laundering.

Warshak appealed the ruling, saying his Fourth Amendment rights were violated when investigators failed to obtain a warrant for his emails. In its ruling Tuesday, the Sixth Circuit Court of Appeals agreed with Warshak and effectively declared parts of the Stored Communications Act to be unconstitutional.

However, the court also said that law enforcement agents “acted in good faith” in using the Stored Communications Act to obtain the emails, so it will not vacate Warshak’s conviction. ZDNet reports that he may see a lesser sentence as a result.

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“Today’s decision is the only federal appellate decision currently on the books that squarely rules on this critically important privacy issue, an issue made all the more important by the fact that current federal law … allows the government to secretly obtain emails without a warrant in many situations,” the EFF said in a statement.

“We hope that this ruling will spur Congress to update that law … so that when the government secretly demands someone’s email without probable cause, the email provider can confidently say: ‘Come back with a warrant.'”