The Environment Department says a recent survey found the herd's population had dwindled to an all-time low at about 20 animals.
The province says it has amended an agreement with Nalcor Energy, which is working in the Red Wine Mountain area to complete the Muskrat Falls hydroelectric project.
The department says changes to an economic activity permit are aimed at minimizing disturbances to the remaining animals.
Environment Minister Dan Crummell says the Crown corporation must increase its monitoring of the herd and limit work during certain times.
Among other things, the amended permit says the Nalcor must reschedule work if caribou are seen within a four-kilometre radius of the work area.