The company, a division of online auction company eBay Inc, posted on its website that many of its users were "having problems" logging into the free service.
"Our engineering team has determined that it's a software issue," a posting by Villu Arak on a blog maintained by Skype said. "We expect this to be resolved within 12 to 24 hours."
It was not immediately clear how many users were affected, but Skype users in Colombia, Brazil, Germany, Finland and the United States reported difficulties logging on.
There were 29 posts on the same blog lamenting the lack of connections.
Skype urged users to keep the program running "and as soon as the issue is resolved, you will be logged in. We apologise for the inconvenience".
It also temporarily disabled downloads for the program, but said they would be made available "again as quickly as possible".
Skype, was founded by Niklas Zennstroem and Janus Friis, and uses peer-to-peer technology to connect phone calls, instant messages and videos between its users.
It runs on a variety of operating systems, including Windows, Mac OS X, PocketPC and Linux.
Besides computer-to-computer calls, Skype users can also use the program to connect to cellphones and traditional landline telephones.
The company was acquired by eBay in October 2005 for about $2.1bn.