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Fisheries and Oceans Canada is computerizing its licensing services starting next year. (CBC)

Fisheries and Oceans Canada is computerizing its licensing services, prompting some organizations to worry about "mass confusion" for thousands of fishermen across the country.

Over-the-counter services for licence renewals and payments at Fisheries and Oceans offices across Canada will end as of Jan. 2, 2013.

"Fishers will be able to use the same system to access most in-season licensing services, including approval of designations," Frank Stanek, a spokesman for the department, told CBC News in an email.

"The web-based system will replace existing counter service for licence applications and renewals, including in-person payments of licence fees at Fisheries and Oceans Canada offices."

Nellie Baker Stevens, who represents more than 200 fishermen in the Eastern Shore Fishermen's Protective Association, said the new system — called CanFis — had been considered for years but was only presented as a plan about a month ago.

"It'll be mass confusion," she told CBC News on Tuesday.

"Here it is that we're going to be losing our services to our fishermen."

Dave Theriault, who fishes out of Three Fathom Harbour on the Eastern Shore, said he predicts lengthy delays at his computer before he eventually masters the licensing program.

"It's a big pile of stress because if you mess up on to it, you're not sure that it's actually going to the right person," he said.

"When I use a computer, I use one finger at a time."