It is generally assumed that Skype calls cannot be tapped and since the company uses 256 bit encryption Skype calls are twice as secure as many internet credit card transactions. According to this story, Kurt Sauer, Skype’s chief security officer says, there are no "back doors" that could let a government bypass the encryption on a call. At the same time, he said Skype "cooperates fully with all lawful requests from relevant authorities." He would not give particulars on the type of support provided.
So if the government has an IP address of a person on a Skype call and the cooperation of the ISP they are able to record all packets going to that address. They may even be able to do this without proactive ISP cooperation. At this point, since they have Skype’s help, they may be able to unencrypt the call. In theory they could also ask Skype to send duplicate voice packets destined for specific callers to a government agency.
So while many view VoIP as a technology that makes the government’s job more difficult, it may actually make it easier in certain cases. After all, IP makes it easier to record remote call center agent conversations, the same thing can be true of wire tapping.
Since Skype is now owned by eBay I can’t imagine a scenario where they aren’t giving the government the keys to their encryption system. After all CALEA may not apply officially to Skype calls that stay on network but Skype would likely still comply or risk major government problems.