In 2000 the Cook Islands' Government began to pay 75% of teachers' salaries and running costs in all private and church schools.

At the same time the schools' principal, Brother Norman Gillies established a charitable trust to ensure a regular supplementary income for future maintenance and development.

Later that year the block was rebuilt with funds supplied by the New Zealand Government through the Cook Islands Investment Commission (CIIC).

[10] On Sunday 20 October 2013, a deliberately-lit fire destroyed a classroom block representing two-thirds of the college's teaching space.

[11][12] The difficulties of providing teaching and learning areas for the students and teachers was dealt with in 2014 when the college rented a marquee for the year and in 2015 a movable classroom was built.

Negotiations took place between the government of the Cook Islands, the school board, the Catholic Church and the landowners for the continued occupation of the land.

[13] St. Joseph's Catholic Cathedral at Avarua, located near Nukutere College, was also affected by the same land problem and benefitted from the same solution.

Delaney Yaqona, the principal of the college, said, "this is a new beginning for Nukutere this is the start of the rebuild; thank you to the landowners for the peaceful negotiations, the Catholic community, all the teachers, students and the parents".

"Earth rocks" selected from the Arai-Te-Tonga marae were laid into the foundation by Deputy Prime Minister Mark Brown, Munukoa Purea, Chairman of the school board, Bishop Donaghue, Mike Savage, and Sister Elizabeth.

Bishop Donoghue also placed a jar holding a statue of Saint Joseph and a list of names of every student of the college present at the occasion into the foundation trench.