Muliaina, 29, will have February off, missing the Chiefs' three matches on the road against the Sharks and Lions in South Africa and against the Western Force in Perth.
The Chiefs captain and veteren of 77 tests asked for the clause in his contract when it was renewed with the NZRU earlier this year.
NZRU chief executive Steve Tew told the Sunday Star Times that Muliaina's exemption was a rare one.
"Although Mils is likely to have extended leave at the beginning of Super rugby, he is just one player out of 140," Tew said.
"We have made it very clear, as the Australians and South Africans have in their own way, that we will have to take a case-by-case look at our players if they are going to survive."