NZR sold ownership of the management licences of their five Super Rugby franchises from 2013, with the sale split between the team's component provincial unions and private investors.
The Auckland, North Harbour and Northland rugby unions bought a 60 percent stake in the Blues in 2013, with private investment group Bolton Equities Limited (BEL) purchasing the other 40 percent.
The agreement was supposed to run for seven years but on Friday NZR said they had taken back ownership of the BEL shareholding following a review of the Blues' governance structure and their on-field performances.
"The review concluded that the existing shareholding mix is unsustainable and due to NZR's overriding commitment to the provincial union shareholders, has recommended that BEL sell its shares to NZR," the national governing body said in a statement.
"On that advice, BEL has agreed to exit the partnership on the basis that this will allow NZR to work with the provincial union shareholders to find a new group of investors."
NZR added they had purchased the shareholding on a temporary basis, with an eye to securing new private investment in consultation with the three provincial unions.
"NZR has agreed with the remaining Blues owners to hold its partnership interest until a process has been completed to identify alternative private investors," NZR said.
The Blues have been the worst-performing New Zealand side in Super Rugby since 2013.
They have failed to make the playoffs in each of the years since and finished ninth in a reduced competition of 15 teams this year with seven wins.
They have also been criticised for poor recruitment and talent development, with several players within the wider Auckland area leaving and going on to earn All Blacks honours from other Super Rugby sides.
Crowds have also fallen away after years of mediocre performances and the Auckland-based New Zealand Herald said on Friday there was a concern that playing numbers and the sport's support were falling away in the country's largest city.
(Reporting by Greg Stutchbury; Editing by Peter Rutherford)
