The ban, which began in April and will now run to October, has been tightened to include passenger boats and other vessels with more than 100 passengers and crew, the ministry of transport said in a statement. The original ban was on vessels with a capacity of 500 or more people.
The move will deal a blow to several Canadian cities such as Vancouver, Quebec and Montreal, where the cruise industry makes an important economic contribution.
In 2019, Canada was visited by 140 cruise ships from a dozen countries with some two million tourists on board, according to the ministry.
Small boats for short excursions, such as whale watching, will however be allowed to resume their activities starting on July 1, in line with permission by provincial and local authorities.
Nevertheless, the movement of vessels with a capacity of more than 12 people will be banned from Arctic coastal water until October 31.
These rules do not apply to small craft used by local communities for transport or fishing.
Ferries, deemed essential services, will be allowed to continue operating but will have to implement safety measures to curb the spread of the disease.
Anyone caught violating the ban faces a fine of Can$5,000 ($3,600) per day for individuals and Can$25,000 for businesses.
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