But until Edward Snowden leaked NSA documents that stated that Skype entered its PRISM program in early 2011 (before being acquired by Microsoft), there was no public proof that such a thing has actually happened.
The New York Times' sources have revealed that various companies, including Skype, have been known to cobble together secret in-house teams that would look into ways of allowing these agencies access to the requested user data even before they ask.
Skype's secret program was (is?) named Project Chess, and was started some five years ago, when the company was still in the hands of eBay.
So, yes, the denial that corporate vice president in the Microsoft Skype Division Mark Gillett wrote last year could be technically correct and that it's true that Microsoft wasn't the instigator for making Skype snooping easier for the agencies.
It was Skype all along. Although, given Microsoft's own participation in PRISM, the distinction seems irrelevant.
The ultimate point of all this is that people have been hearing lately a lot of denials from various companies and agencies, but fewer and fewer trust them. The EFF has two good postsabout NSA’s "word games," which can definitely in part apply to the private sector companies.