Muralitharan, out of Test cricket since August last year, was not included in an 18-man training squad for the two-Test tour which was postponed from January due to the Asian tsunamis which ravaged Sri Lanka on December 26.
The 32-year-old, who underwent corrective surgery last month, will target a return with English County Lancashire after getting married to an Indian girl later this month.
"It is unfortunate Murali will not be around in New Zealand, but he needs time to recover," Sri Lanka's chairman of selectors Asantha De Mel said on Thursday.
The off-spinner claimed a world record 532 victims in 91 Tests before the injury, but was later surpassed by Australian leg-spinner Shane Warne who has so far grabbed 567 wickets in 121 Test matches.
Muralitharan played his first international match since August when he turned out for an Asian XI against a World XI in the tsunami charity One-dayer in Melbourne in Australia in January.
But doctors ordered minor surgery on the right shoulder when the pain resurfaced after the match.
The two Test matches on the New Zealand tour will be played in Napier (April 4-8) and Wellington (April 11-15).
The training squad, expected to be pruned to 14 next week, also does not include left-arm seamer Nuwan Zoysa who is recovering from a knee injury.
"We will be looking to bring about a balance for the two Tests with six batsmen, one all-rounder and four bowlers," said De Mel.
Sri Lanka's 18-man squad:
Marvan Atapattu (capt), Mahela Jayawardene, Sanath Jayasuriya, Kumar Sangakkara, Tillakaratne Dilshan, Thilan Samaraweera, Ian Daniel, Chaminda Vaas, Lasith Malinga, Nuwan Kulasekera, Farveez Maharoof, Upul Chandana, Rangana Herath, Thilina Kandamby, Avishka Gunawardene, Dilhara Fernando, Gayan Wijekoon, Ruchira Perera.