At the moment, it's unknown as to how FBI investigators managed to obtain access to these Skype chat logs. Skype itself says it only stores the IM chat logs of its users for up to 30 days. Skype said they were not asked by the FBI to turn over any files and were never served with any court papers by the government.
The article hints that the FBI might have installed some kind of spyware on the PCs of Megaupload employees...
Sources