Some 12 ScotRail trains on five routes into the station, including the main line from Edinburgh, were cancelled.
Others services were delayed on the Aberdeen, Dunblane, Cumbernauld and Anniesland via Maryhill lines for a total of several hours.
The disruption was caused by a track measurement train operated by Network Rail finding a defect with a rail at Greenhill junction in North Lanarkshire overnight.
The train then leaked fuel as it travelled through the steep tunnel down into Queen Street station, which caused problems for other trains climbing the incline.
A spokesman for Network Rail said: “Issues first thing at Queen Street were caused by poor railhead conditions. A train passing through the tunnel overnight shed some fuel and trains then had trouble climbing through the tunnel as a result.
“The current problems are due to a rail defect at Greenhill. ScotRail has agreed to cancel off a few trains to allow engineers access.”
A spokeswoman for ScotRail said: “Due to poor rail conditions at Glasgow Queen Street High Level station this morning, services are disrupted.
“We apologise to customers for any inconvenience caused by circumstances outwith our control.”