"It wasn't pretty to see," one reindeer rancher, Ingmar Blind, told state television network SVT.
The animals, which provide a livelihood for many in remote northern Sweden, met their fate on Saturday near the village of Kaitum in the country's Laponia region.
Near-misses by railways are common as herds migrate during winter in search of food.
But in this case it appeared the herd had wandered onto snow-covered tracks and were startled by the train, the regional transport official in charge of maintenance, Fredrik Rosendahl, told AFP.
The reindeer instinctively all ran along the tracks before the train, which crushed them.
"If you follow a reindeer in a car, for instance, it will tend to run in front of the car, it won't go to one side," Rosendahl explained. "So just imagine what happens with a train that needs more than a kilometre to come to a stop."
While the extent of the carnage in Saturday's train-reindeer collision was unique in its scope, reindeer herders have long complained about the fatal consequences of increased rail traffic in Sweden's far north.
Back in 2012, a new high-speed rail line claimed the lives of an estimated 200 reindeer in its first three months of operation, prompting one herder to compare the train to a meat grinder.