Skype is an IT manager's nightmare. For one thing, Skype encrypts all its traffic, which makes it impossible to monitor what employees are doing, sending, or saying when they use this communications tool. In addition, Skype doesn't follow the path of most VOIP services. It enters the corporate network as an application embedded in a mobile device; it is activated whenever a user accesses the Internet from within the corporate network to make a call. In this way, Skype could open holes in a corporate firewall from the inside. The fear is that Skype users could expose corporate networks to hackers, viruses, and malicious software ("malware"), or shield the activities of malicious employees.
The world is moving towards peer-to-peer, not just in VOIP but in many many ways. I'm willing to bet that for many companies, the cost savings will trump the potential security issues. And let's face it, if you are really worried about the "activities of malicious employees" then isn't something wrong with your hiring process?