Problems with payroll for employees of the Alaska Marine Highway System may soon be shipping out, thanks to a shift in the accounting departments and how payroll is managed.

“The good news is that we’re pulling that into DOT,” said Craig Tornga, marine director of AMHS, which operates under the Department of Transportation and Public Facilities. Payroll had been managed under the Department of Administration, which oversees payroll for some 14,000 state employees.

[Also in this series: AMHS steers fleet toward three replacements | The cost of maintaining an aging ferry fleet | Meet the fleet]

[Part 1: Help wanted on the Alaska Marine Highway | Meet some of tbe crew on the Columbia | New program puts retired troopers aboard]

For the better part of two years complaints have been piling up about incomplete paychecks — or none at all. It prompted some people to quit and deterred others from seeking employment with AMHS, at a time when it sorely needs licensed workers. Members at the Marine Engineers’ Beneficial Association union hall in Seattle, for instance, were telling people not to work for AMHS because pay wasn’t reliable.

Tornga said it got to the point that every time he went to a boat he heard from someone about a problem with their paycheck.

“It was disheartening. We lost a lot of good people with frustration over pay,” he said. He added that his boss, DOT Commissioner Ryan Anderson, facilitated the solution, which should be implemented with the first paycheck employees receive this month.

Crew interviewed in July said the key issue with payroll was likely the complexity of managing the ferry system payroll, which among other things is determined by three different union contracts. With the crew shortage, more paychecks change every cycle. There is also a lot of irregular pay since some crew work relief and others work on “holdover” where they stay on after the contracted time.

One exasperating factor, Tornga said, was that a lot of crew reported calling or emailing to find out what was wrong, and what they could do to fix it, without anyone calling them back.

He cautioned employees against thinking it would be worked out immediately.

“The department has a backlog of payroll to deal with, a lot of cleanup.” Tornga said. It amounts to “dozens of items,” so AMHS employees should be patient a little bit longer.

“We’re very hopeful we’re going to get that behind us,” Tornga said.

• Contact Meredith Jordan at meredith.jordan@juneauempire.com or (907) 615-3190.