Thursday's order comes after Gov. Brian Schweitzer's administration transferred 62 Yellowstone bison to the Fort Peck Reservation earlier this week.
The ruling presents another stumbling block in efforts by tribes and agencies to reintroduce bison to parts of their former range.
Half the Fort Peck animals were to be transported from a holding pen in coming months to the Fort Belknap Reservation, and dozens more are being held temporarily on Ted Turner's ranch near Bozeman.
The judge blocked those transfers, at least for now, but turned down a request to return the animals to the Yellowstone area and set a hearing for April 11.
