Managing director of Flight Centre David Coombes said it was an incredibly difficult decision to make.
"This restructure will be mostly within our retail arm, given the lack of work available for our people based in our stores right now. Our people were offered, and a number accepted, voluntary redundancy."
Coombes said these people will be able to access the Government's Covid-19 relief fund, with those who wished to stay with the business being offered a role.
"We are gutted to again be reducing our team and farewelling a large number of talented and passionate people from our business. Our people are at the core of who we are, so this is of course, heartbreaking."
A Flight Centre spokeswoman said it isn't clear how many would be affected from the Whanganui branch as some may accept roles at another branch.
The store is set to close at the end of October.