Yes you can. Just as you can create an app for the public appstore you can also create it for a company specific app store. It is sometimes even easier because you do not have to jump to all kinds of hoops that normally apply in the public appstore.
The only tricky part is to connect your developer account to the company appstore. That took me some time to figure out on how to do that. But once that is done the process of publishing your app is almost the same.