The deal aimed to stem losses on the Bern-based company’s trains running through the Gotthard tunnel.
Starting in 2014, BLS Cargo will operate 10 fewer trains daily through the tunnel.
As a result, 60 locomotive drivers will lose their jobs.
BLS Cargo, which specializes in hauling freight through the Alps, lost 1.85 million francs in 2012.
The company blamed low prices and the strong value of the franc against the euro for the loss, in addition to high rail access rates for the red ink.
Directly and indirectly, BLS Cargo employs about 400 people.
The company says that it cooperates closely with DB Schenker Rail for joint cross-border arrangements that involve planning the use of locomotives and drivers together.
BLS Cargo is majority owned by BLS AG, a transport group that operates passenger trains, buses and boats in Central Switzerland.