Ex-cyclone Ellie is bringing heavy rain to parts of the Northern Territory, with the weather bureau issuing a warning for flash flooding.

The category one storm made landfall in the early hours of Friday and has since been downgraded to a tropical low.

But the Bureau of Meteorology is warning up to 250 millimetres of rain could still fall across the Carpentaria, Tanami and Barkly districts this weekend.

Up to 120mm could lash parts of the state within six-hour periods, while thunderstorms and heavy winds could also affect the towns of Tennant Creek, Wadeye, Nauiyu, Lajamanu, Elliott and Kalkarindji.

The bureau is advising NT residents to secure loose outside objects, seek shelter if conditions deteriorate, and avoid driving into water of unknown depths and currents.

Swollen Murray

It comes as separate flood warnings remain in place for northeast parts of South Australia.

Up to 220 gigalitres of water has reached the SA border from the Murray River, with the river expected to stay at a major flood level for some weeks.

Those in Renmark and surrounding towns should prepare their homes for flooding and consider leaving the area, SA’s State Emergency Service has advised.

The emergency service is warning the flood water will remain in the region for some weeks, so people choosing to stay must have enough food, water, fuel and medication.

-AAP