You are going to need to be more specific.
If you are talking about Windows Messenger with the exchange version, that is supported only in exchange 2000 and administration takes place on whatever server you have running that service for your organization. You can also check the properties in Active Directory to make sure they are enabled for instant messenger or if someone has disabled the user for some reason in which case you can re-enable the account as well.
If you are talking about Live Communications, that again will be administered from the Live Communications server. Again, check the user’s properties in AD and make sure they are enabled.
I can’t really give you a definitive answer when you have given no details as to your verion of exchange and what you mean exactly by messenger. Please fill in the details first. Thanks.