Treasury officials say the extra $35 million in the budget for private schools won't improve choice or educational outcomes.
Newly-released Treasury papers show the government was advised not to give more money to private schools, one of National's key election promises for education.
The government said the extra money would make private schools more affordable for parents.
The Treasury also questioned the tagging of $36 million for the government's controversial new national standards for primary schools.
The papers recommended deferring the funding for another year because they say there is no information to effectively target funding to the schools that need it most.