The Northstar Commuter rail got off to a bad start again this week, with delays of up to 90 minutes.
Metro Transit said the long waits result from BNSF Railway freight traffic that shares the same rails.
They follow delays of earlier this month when freight trains stalled due to cold weather. Last week, trains hit cars stalled on the tracks two days in a row.
"We are expecting that we'll be working with BNSF to take care of this afternoon's commute," Metro Transit spokesman Drew Kerr said. "The rest of the week we expect that the trains will be operating, and we hope that our customers will stick with us. We really thank them for their patience and hope that they'll continue to ride."
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Northstar Commuter rail began operation in November 2009, and has been among the most reliable transit options in the Twin Cities until this winter.
Freight congestion and frozen railroad equipment have been the primary problems. The 40-mile Northstar line runs from downtown St. Paul to Big Lake.
Kerr said the agency's power to clear the way is limited. He said officials are working to keep commuters informed so they can make decisions about travel.
"One of the best things we're doing right now is communicating with our customers and letting them know about the issues that we're facing, and letting them know in real time exactly what they can expect as they head to work in the morning, and come home in the evening," he said.