The Cook Islands Finance Minister, Sir Terepai Maoate says lack of leadership within the Ministry of Works and Outer Islands Ministry was the main push behind merging the two.
An audit report identified a lack of networking among ministries and agencies, communication breakdowns, and absence of time lines on outer island projects.
Sir Terepai says over the past two or three years there's been a lack of progress on infrastructure projects despite efforts to get them going.
"We tried all sorts of things to make things happen but it didn't happen so we put in a committee to review these two ministeries and the outcome of that was a recommendation to merge the two, because there are quite a few people engineers, technical people in there that can do the job but what's lacking is leadership."
The Cook Islands government will be seeking a loan to complete infrastructure projects for the main and outer islands.