GO Transit riders faced delays on the Lakeshore train line for the second day in a row Wednesday.

The public transit system struggled on Tuesday, the first day back to work for many Torontonians, with multiple train delays on the Lakeshore line blamed on employee cuts.

Difficulties continued for the train line with four Lakeshore East trains delayed more than 15 minutes Wednesday morning, and one trip from Oshawa late by 78 minutes because of equipment problems, the company website said. A Lakeshore West train to Burlington was also late by 20 minutes.

The Canadian National Railway Co., which provides crews for Lakeshore trains, recently cut the number of engineers on each train from two to one at the request of GO Transit to save money.

Crews had consisted of four workers — two engineers, a conductor and an assistant conductor — but under the restructuring have been cut to three.

"With new procedures, we just basically had some teething problems in terms of getting up to speed," said CN Railway spokesman Mark Hallman.

Two unions — Teamsters Canada Rail Conference, which represents engineers, and the United Transportation Canada, which represents conductors — filed grievances about GO's request for the change, but a federal labour arbitrator ruled Friday that the decision fell within the collective agreement.

The restructuring means 34 engineers have been reassigned from GO trains to CN's freight service.

CN spokesman Hallman says that everybody is still getting "up to speed with the new procedures." But he adds that train service improved as the day progressed Tuesday, with peak on-time performance at 91 per cent.

Ed Drass, a transit columnist with Toronto's Metro newspaper, fears recent delays may indicate long-term problems for riders in the year ahead.

He says riders have been warned that transit may face a rough road ahead, in part because of construction.

"Riders will have to deal with some serious delays that they're not used to," says Drass. "You'll get delays from signal issues, construction, and now the added concern is that there are staff issues not only with the trains but with the buses."

Crew shortages Tuesday also caused GO Transit bus cancellations and delays.

Drass says if that's the problem, the company will have a tough time filling those positions.

"Not only is the professional driver position in demand for buses, but it's also with the freight companies," Drass said. "Trains, trucks — everyone needs employees right now right across the continent."