Tuipulotu was sent home from the All Blacks end of season tour last November after testing positive for an unspecified banned substance. The team said at the time he had departed for "personal reasons".
NZR and the New Zealand Rugby Players' Association (NZRPA) issued a statement confirming the positive test after a report in the local media on Sunday.
"NZR and NZRPA can confirm that, in November 2016, they were notified that a doping control sample provided by Patrick Tuipulotu had, reportedly, revealed the presence of a specified substance listed on (WADA)'s prohibited list," the statement said.
"Patrick was shocked by the test result and is working hard to identify the source of the specified substance. In accordance with WADA regulations, Patrick remains provisionally suspended pending resolution of this matter.
"Further to these regulations, NZR and NZPRA are bound by strict confidentiality obligations."
The 24-year-old Tuipulotu made his All Blacks debut in 2014 and was in contention for the 2015 World Cup squad but underwent surgery for a congenital hip problem and missed most of the season.
He returned to the national team last year but returned home early after he played his 12th test in the 68-10 victory over Italy in November.
Tuipulotu has not reported to his Super Rugby side for pre-season training due to the provisional ban, the Auckland Blues also blaming an "ongoing personal matter" for his absence.
World Rugby are signatories to the World Anti-Doping Agency Code and, as a first-time offender, he could face sanctions ranging from a warning to a two-year ban.
Former women's sevens player Lavinia Gould was the first New Zealand international to receive a ban for doping in 2013 after she tested positive for methylhexaneamine.
Two lower-level club players were also suspended last year for possession and use of banned anabolic agents.
According to WADA statistics for 2015, anti-doping agencies conducted 8,451 urine and blood tests worldwide on rugby players, with 80 adverse analytical findings. More than half of those were for anabolic agents.
Drug Free Sport New Zealand (DFSNZ) conducted 355 tests on rugby players in New Zealand in 2015, with just two adverse findings.
Former WADA director general David Howman however has warned that testing probably did not extend far enough, with the possibility of secondary school players using anabolic agents or banned supplements to add muscle bulk.
"Kids are doing it. That's the part that scares the hell out of me," New Zealander Howman told Fairfax Media last year before he left WADA.
"We don't do a lot of testing of kids in that region, 15 to 16, First XV ... and that probably is the area which is most vulnerable."
(Reporting by Greg Stutchbury in Napier, New Zealand; Editing by Nick Mulvenney)
