The new $3-million web-based system was set to launch Jan. 1 but was pushed back.
Melanie Sonnenberg, the co-ordinator with the Eastern Fishermen's Federation, said fishermen across the Maritimes will feel the impact of this new government licensing system.
"Because this has been so driven from the top and pushed downward," she said.
As for consultation with fishermen, Sonnenberg said, "has not occurred on any of this."
Once the online program is up and running each fisherman will get an individual pass code so they can look at their holdings, renew licences and make payments online.
Over-the-counter service for licence renewals and payments at offices across Canada will end once the internet-based system is operating.
The online licence system is one of several changes being introduced in 2013 as the federal government transfers the cost of managing the fishery from taxpayers onto the industry.
Beginning in May, lobster fishermen will have to pay for lobster trap tags and find suppliers.
Another change set to come in April 1 is the federal government will no longer contribute to the at-sea-observer program, which requires some boats to carry independent fisheries observers.
Sonnenberg said that's a problem.
"There doesn't seem to be any acknowledgment by the department that any of this is a problem. It's been a very frustrating time and I think it will become more frustrating on April 1," she said.
A Fisheries and Oceans Canada spokesperson said in an email the department is working to ensure the most "efficient service for fishermen."
The changes to management programs follow cuts to the Fisheries and Oceans Canada's budget last year.
In 2012, the department's budget was cut by $79 million as part of the national deficit reduction plan.