It was pegged to cost $5.5 million in 2014/2015 and $74 million in this financial year, with the remaining money spent over the next two years.
However, Mr Hipkins said this morning figures showed only $4.7 million has been spent so far. Of that $983,000 was spent in the last financial year, and $3.8m this year. If the project was on schedule, that figure would be around $50 million, he said.
Minister of Education Hekia Parata said the delay in spending was due to industrial negotiations aiming to secure full sector support "and to give schools time to build relationships before they engage in the development of their achievement challenges".
The Ministry of Education was now re-phasing funding to reflect the delay in appointments to the new roles and the related payment of additional allowances, the minister said.
Funding was also being reorganised to meet the higher-than-expected number of schools forming "communities of learning". So far, 789 schools had signed up, or about one third of all schools in the country.
The Ministry of Education's Head of Sector Enablement and Support Katrina Casey refuted allegations the policy implementation was behind schedule.
She said IES was now travelling at pace, with 11 communities having challenges endorsed.
To date almost 90 principals and teachers had been appointed to the new roles, Ms Casey said.
However Mr Hipkins said claiming the delays weren't the Government's fault was shifting the blame.
"It only goes to show their incompetence at implementing new ideas in the education sphere, along with the Novopay disaster and charter schools," he said.
"As John Key announces more promises in his latest speech, he's still not delivering on the promises he made two years ago."