The All Blacks legend damaged his Achilles tendon in last weekend's 19-13 defeat to the Ospreys in the RaboDirect Pro12.
A Munster statement said: "Doug Howlett will have a scan and see a specialist early this week to determine the exact nature of the injury he sustained against Ospreys.
"Initial examination suggests he's damaged his Achilles tendon and he has definitely been ruled out of Munster's upcoming Heineken Cup matches against Scarlets."
Munster travel to Parc y Scarlets on Saturday, with both teams boasting 100 per cent records after the opening two rounds of games.
The Scarlets also have injury concerns regarding one of their wings, after George North limped off towards the end of Wales' defeat to Australia.
The Welsh region had five players in the match 22, while centre Jonathan Davies missed the game with a groin complaint.
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