Flights to St. John's, London, Ont., Lloydminster, Alta. and Medicine Hat, Alta. will be suspended beginning March 19.
A lack of targeted help for airlines and airports, combined with a near-total shutdown of travel, could mean permanent closures.
Canada's new COVID-19 testing policy led to unprecedented travel cancellations, the airline says.
The online shopping giant had previously only rented jets.
The airline has also suspended the Toronto-Quebec City route.
The maximum weekly pay for employees on CEWS will drop to $400 per week, down from $847, WestJet said.
The Canadian airline is changing its policy months into the pandemic.
This is the first time Transport Canada has imposed the financial penalty for breaking rules aimed at slowing the spread of COVID-19.
The airline implemented a zero-tolerance rule when it comes to face coverings.
The airlines had blocked the sale of adjacent seats in economy class.