The 33-year-old former Blues full-back is set to undergo surgery after scans revealed he had ruptured his Achilles.
Howlett suffered the injury in the closing minutes of Saturday's 19-13 loss to Ospreys.
Howlett now joins Felix Jones, David Wallace, Jerry Flannery and Darragh Hurley in facing a lengthy spell out of action.
There is some good news for Munster, though, with Keith Earls, Peter Borlase and Dave O'Callaghan all closing in on comebacks.
Earls should return to full training next week while Borlase and O'Callaghan are poised to play for the club's second string in the British & Irish Cup game against Ayr on Saturday.