Union director Gavin McGarrigle questions how well the new system will work, without the centre overlooking the region from its base atop a commercial tower at 555 West Hastings Street, overlooking Burrard Inlet and English Bay.
"As we say to people who live in Vancouver, 'How would you like to land at the airport and know that your control tower was based in Victoria?'"
The closure is part of a plan announced in 2012 to reorganize Coast Guard operations, including the controversial closure of the Kitsilano Coast Guard Station.
The plan included closing 10 marine communications centres across the country, and upgrading the technology in the 12 remaining centres to manage a wider area.
On the West Coast the communications operations will be consolidated at upgraded centres in Victoria and Prince Rupert.
The Tofino centre, which was actually located in nearby Ucluelet, closed on April 21. The Comox centre will shut down sometime in early 2016.
Marine traffic around Metro Vancouver is also monitored by Port Metro Vancouver.