Chief Minister Natasha Fyles said communities directly in the path of the cyclone, including Wadeye, Daly River and Peppimenarti had reported no major damage despite wind gusts up to 100 km/h.
Ms Fyles said concern now centred on possible flooding, especially in the Tanami region as the system continued to move south.
"It's now going to be a tropical low, dumping a lot of water on the Northern Territory," she said on Friday.
"As people are moving about for Christmas our clear message is to please take care, heed all warnings from authorities and reconsider all non-essential travel."
Ms Fyles said the Bureau of Meteorology was forecasting 200-300 millimetres of rain over coming days.
"That is months and months of rainfall that's going to fall," she said.
"We don't want to have people in tragic situations where they're bogged and can't get through."
Despite downgrading the system, the bureau still had a severe weather warning in place on Friday for people in Daly, Tiwi, Gregory and parts of the Arnhem, Carpentaria, Tanami and Barkly districts.
It said the heavy rain could lead to flash flooding as monsoonal showers and thunderstorms extended south during Friday afternoon and into Saturday.
Wind gusts of 90 km/h were also possible.
Acting Police Commissioner Murray Smallpage said once Ellie reached land it had not proved as severe as expected with some communities reporting conditions similar to seasonal monsoons.
In Wadeye, the local school had been prepared as a shelter, but was not needed.
