If you are thinking of hosting a web service in IIS only to communicate with an NT service on the same machine, this is definitely more of a problem than it costs in this case.
As pointed out in other answers, you can make the WCF service with the necessary operations and place them in the same NT service that you want to interact with. You can easily provide this with certificates or user accounts to make sure that they are controlled only by the right people / machines.
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