The service outages — one for 18 minutes and another for 27 minutes — are being blamed on old equipment installed in the 1980s and 90s.
"The outages that occurred over the last few days, I wouldn't say they're a normal part of business, but they're not uncommon when you're dealing with older technology," Greg Licke, director of operations in the Victoria communications centre told CBC News.
Licke said that there are plans for the systems to be modernized and updated, but that meanwhile, backup services are in place and that outages do not put those on the water in danger.
The local Kitsilano Coast Guard Station was closed in a round of budget cuts in February 2013. The loss of the search-and-rescue centre has been the subject of much controversy, with many believing its closure leaves Vancouver's coastline in danger.
After the first outage on Sunday, Robin Pascall, a commercial watercraft captain told CBC News he had never seen anything like it.
"The old system obviously worked. This sort of thing would be unheard for traffic to shut down," he says. "It is the marine equivalent of air traffic control saying our radar doesn't work and everyone has to land on their own."
Just last month, a former captain in the coast guard, Tony Toxopeus, told CBC News that the Kitsilano base would have been able to respond almost immediately to an oil spill that polluted the waters of English Bay with bunker fuel from a tanker.
However, the federal government has said the Kitsilano Coast Guard base, which was primarily a search-and-rescue station, was not equipped for oil spill response and maintains its absence had no impact on response times.