Skype’s relationship with the U.S. intelligence establishment is older than its alleged involvement with the NSA’s recently revealed Internet surveillance program PRISM, according to a New York Times report Thursday.

The endeavor, called Project Chess, began five years ago while eBay still owned the company. Project Chess’ aim was “to explore the legal and technical issues in making Skype calls readily available to intelligence agencies and law enforcement officials,” sources told The New York Times.

Earlier this month, The Guardian and The Washington Post reported that Skype was one of nine major Internet companies participating in PRISM under the National Security Agency.

Skype allegedly came on board February 2011 before it was acquired by Microsoft in May 2011. Microsoft reportedly joined the program in September 2007.

Microsoft carefully acknowledged that it complies with orders for data regarding “requests about specific accounts or identifiers” when the company “a legally binding order or subpoena to do so, and never on a voluntary basis.”

“If the government has a broader voluntary national security program to gather customer data, we don’t participate in it,” the company said in a statement to gaming site Kotaku.

The other companies accused of participating — Yahoo, Google, Facebook, PalTalk, YouTube, AOL and Apple — have also issued their own vehement, carefully-worded denials.

Earlier this year, privacy and transparency activists urged Microsoft to come clean about it and Skype’s security practices, user data retention policies and its interpretation of its legal responsibilities to comply with law enforcement requests.

The White House, senior members of the congressional intelligence committees and senior officials of the intelligence community have all defended the legality and effectiveness of the program, as well as the oversight regime holding the program accountable.

Follow Josh on Twitter