The cyclone is expected to bring gale-force winds of around 110km/h over Groote Eylandt on Saturday as it tracks towards the border.
Winds above 125km/h could intensify and could compound the effects of heavy rainfall already expected in the top end over the weekend.
The heaviest falls are expected on coastal and island locations, before reaching further inland into the Carpentaria district.
“While it [the cyclone] is most likely to cross the coast on Monday it will be slow moving making both the timing of landfall and intensity at that time quite uncertain,” the BOM said.
The weather event will then weaken once it makes landfall and is likely to move west through the NT as a tropical low, bringing heavy winds and rain.
Ex-Tropical Cyclone Lincoln dumped heavy rain and winds over the region in February, triggering flood watches and warnings in northwest Queensland, the NT and northern WA before moving offshore.