McNeil said Wednesday the moves are meant to be a signal that his government is changing direction and is serious about implementing its campaign platform, which includes major changes to the education and health-care systems.
"I made it very clear that the commitments that I have made in our platform are going to be delivered," said McNeil.
He said changing deputy ministers allows the new Liberal government to deliver change in a "timely manner."
The Liberals have promised a comprehensive review of the province's school curriculum and a reduction in the number of health boards, cutting them from 10 to two.
"This really was an opportunity for us to start making sure that we are able to deliver the changes that are going to be required for us to get our mandate finished," he said.
McNeil said acting deputy ministers will be appointed until replacements are found. Five other deputy ministers also switched departments.
He said the three deputy ministers who are leaving the government had provisions in their contracts that will see them get severance of one year in salary.
The premier said he also wants to change the direction of Communications Nova Scotia.
"We have very clearly laid out that department will no longer become a propaganda department for the ruling party," he said. "We will be moving back toward its original intention, which was allowing access to government and government services."