Skype really has two elements -- Instant messaging (IM) and voice communication. Many companies do not want employees using any form of IM as they view this as social and not business-focused. Just as our children socialize over IM, employers are concerned about this being a time waster for employees, and there is some truth to this. It is also true, however, that we all have overlap between our work and home lives, and with the technology being so pervasive, it is very difficult -- if not futile -- to place strict limitations. All employers struggle with this, and Skype is just one example. A fair balance is the best compromise, as these tools are not going away, and if this helps employees manage their home and work lives, ultimately they will be more productive.
Things are more complex on the voice side. Skype can be a great cost saver, so why not use it? Again, there is a basic control issue at stake. These calls occur outside the company's phone system, and the activity cannot be tracked. Some industries have compliance issues that extend to voice -- and IM for that matter -- and in these cases, Skype is often blocked for this reason. The more extensively employees use Skype to make or receive calls, the less control employers have over them, making it easier to do things like talk to recruiters, competitors or their friends.
There also more complex issues in terms of how enterprise Skype behaves with your company's network. Since the service runs over the public Internet, quality is difficult to monitor, and can impact bandwidth efficiency, especially if being used for video calling. This is a valid reason why companies do not use services like Skype for customer-facing communications. Interestingly, Skype can be beneficial in terms of costs savings but also sending large files that cannot be sent over the company's network. There is more to it that than this, but that will have to wait until another time.
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