The Canadian Coast Guard says — for the second Christmas in a row — trouble with the pay system for its employees is making it difficult to get work done.

The Phoenix pay system has been a protracted disaster for the federal government.

It's meant some government employees haven't been paid and others have received too much. CBC News in Newfoundland and Labrador has spoken with a coast guard retiree who didn't receive his pension until months after he left the service.

Canadian Coast Guard vessel Louis St. Laurent in St. John's harbour. (Mark Quinn/ CBC) A senior coast guard official said trouble said with the pay system has been particularly hard in Atlantic Canada.

"It's affected our ability to recruit personnel and retain personnel ... so it has affected our ability to provide our core services," said Wade Spurrell, Assistant Commissioner for the Canadian Coast Guard in the Atlantic region.

There have been periods back in the summer where we were unable to have ships at sea. - Wade Spurrell

Canadian Coast Guard Atlantic Headquarters, Southside Base in St. John's Harbour. (Mark Quinn/CBC) "We have a lot of ships' crews, people who work at our marine communications traffic centre and environmental response personnel who who don't work regular nine-to-five, 40-hour-a-week jobs and as a result they've been affected. Their regular pay, their overtime premium pays have all been affected."

Sources have told CBC News that some coast guard vessels have been unable to find crews and even captains because of the payroll trouble.

Spurrell said there have been times when vessels have been tied up or delayed leaving port.

"There have been periods back in the summer where we were unable to have ships at sea or provide services in that way. We have had cases where people decided to leave the Canadian Coast Guard because of the uncertainty in their pay"

We are working as hard as we can to try to make sure our people get paid. - Wade Spurrell

CBC News has also heard that payroll trouble has meant that search and rescue operations have had to rely on vessels that were supposed to be working on buoy maintenance.

"When we have situations where a ship is not available or is delayed we will re-prioritize our program," said Spurrell.

"The end result is we might have to drop a lower priority program, postpone that activity until later, while we focus on providing core emergency services, like search and rescue for example."

The Canadian Coast Guard is asking employees to be patient and it hopes this is the last Christmas it will have to deal with these troubles.

"We are working really hard to try to help our people," said Spurrell.

"We've set up pay issues teams here. We are paying people priority payments if they come forward and ask for an emergency payment because their regular pay has been interrupted. We are working as hard as we can to try to make sure our people get paid."