The World Cup winner has struggled to nail down a starting position since his summer signing from Wasps.
Munster Rugby can confirm that Malakai Fekitoa will depart at the end of the campaign after one year at the province.
So far this season, Malakai has made 11 Munster appearances including nine starts, playing at inside centre and outside centre.
He made his Champions Cup debut for Munster away to Toulouse last month and featured in the historic victory over South Africa at Páirc Uí Chaoimh in November.
A World Cup winner with New Zealand in 2015, Malakai represents his native Tonga at international level.
However, things have not gone to plan with fellow summer signing Antoine Frisch forcing his way into the regular XV alongside Jack Crowley.
Munster return to action this Friday where they host Ospreys in Thomond Park. The Irish province have the Cell C Sharks in the Round of 16 in the Champions Cup in April.