The Warriors only had two Duncan Weir penalties to show for a dominant first-half performance that saw them go in at the break 6-3 to the good.
The defeat ends Glasgow's 100 per cent start to the RaboDirect PRO12 season and Townsend admitted his side could have done more to preserve their record.
"We had looked okay in the first-half but couldn't kick on when we had to," he said.
"To be truthful I feel very sorry for the fans. It was a poor performance from two teams at the top of the league."
"That was old school Munster tonight. Over the last 10-15 years the best club side in Europe at holding onto a lead has been Munster.
"We know the effort that's required to win these games. Sometimes things don't go your way.
"We obviously dropped a few balls in the first-half, made a couple of defensive errors in the second-half, and that was enough to put Munster ahead.
"I thought in the first-half we were playing well enough to win the game and we just needed to kick on in the second-half, but we weren't capable of that."