The order was made today by navy commander Vice-Admiral Mark Norman, and it follows an order in July for HMCS Whitehorse to abandon an exercise in San Diego and return to port in Canada following three allegations of drunken misconduct.
Norman said the policy change will help prevent instances of alcohol-fuelled misconduct.
"Alcohol is always a factor that we cannot ignore, but this is not about alcohol," said Norman.
"This is about the conduct of our people and unfortunately alcohol does contribute to misconduct and has done in the past. And we just want to try and regulate that as best we can going forward."
The order will forbid the long-standing practice of easy and cheap access to beer and wine aboard navy vessels. Before today, sailors were allowed to drink while at sea, provided they were not on duty in less than six hours. Beer was available in pop machines on some vessels.
The Royal Canadian Navy on Friday posted an executive summary of the report into the incident online.