Mr Allen said changes were made after staff feedback prompted a "reassessment" of policy positions and strategic priorities.
He said the restructure was still on track to save $24 million.
"The process has been a challenging one, but now that the change programme is confirmed and staff will have greater certainty, we can move forward."
Savings would be made through modernising administration processes and implementing programmes to develop deeper expertise and specialist knowledge, Mr Allen said.
"The decision will also provide opportunities for talented staff to progress their Foreign Service career."
Foreign Service Association Warren Fraser said he still held deep concerns about the proposals.
"These job losses will impact on staff workload and the delivery of foreign and trade policy and we know there are further cuts in the pipeline. It is uncertain whether a restructured Ministry can continue to deliver high quality outcomes for New Zealand.
"The restructuring process has already sparked an exodus of highly skilled and experienced staff. Staff morale is very low and we could see more people choosing to leave."
PSA National Secretary Brenda Pilott said the scaled back restructuring plan reflected the fierce opposition to the original plans.
"This is no cause for celebration... This is yet another indication that public sector restructuring is about cutting jobs, not about better public services."
- Herald Online