I've had a similar problem since upgrading from early 2011 MacBook Pro with Snow Leopard directly to Mountain Lion (did the upgrade a couple of weeks ago). Gradually more and more time has been spent with the fan running until it really started affecting batter power over the last couple of days.
I seem to have found a solution from another thread using Disk Utility and repairing my disk permissions. Perhaps the upgrade didn't resolve all disk permissions to ML's liking. Anyway, after repairing disk permissions and shutting down for a few minutes and restarting, fan usage seems to have reverted to normal.
The thread I was originally at is located here:
https://discussions.apple.com/thread/4155237?start=0&tstart=0