It arrived about 5pm after it was disconnected from a derailed wagon at the rear of the train early in the afternoon.
Dunedin Railways Ltd chief executive officer Craig Osborne said everyone on board was safe.
"No passengers or staff were injured when the wagon popped off.''
Mr Osborne said maintenance and operations staff worked with a crane operator to lift the carriage back on to the track.
They were now repairing the site, and both the Taieri Gorge train and line were expected to be fully operational again today, he said.
However at 1.20pm, just north of Mosigel, the train tried to change tracks at a slow speed to allow another past in the opposite direction and the baggage car came off the rails, Mr Sutherland said.
"We've just been shunting back and forwards."
It was not too much of a hassle, he said.
"We've got a couple of kids, they are pretty excited about it, they're playing cards so they're happy."
Some cruise ship passengers were likely annoyed they could not make it out into the gorge as the track was blocked both ways, he said.