A cyclone watch on Tuesday has been issued for Northern Territory coast areas in Australia.

According to Bureau of Meteorology (BoM), a tropical low hovering between Darwin and Katherine will in all likelihood become a category one cyclone, with winds of up to 125km/h, when it reaches the Northern Territory coast by 10pm (CST) on Wednesday.

The cyclone watch covers coastal areas from the Daly River mouth to Goulburn Island, including Darwin, Croker Island and the Tiwi Islands.

Another watch was issued by the bureau indicating the cyclone could hit Bathurst Island by 10am (CST) on Thursday.

"It's reasonably probable that the low could form into a cyclone but nothing's ever certain here," BoM regional director Andrew Tupper told Herald Sun on Tuesday.

"We've got a severe weather warning out for flash flooding and more strong wind gusts of up to 95km/h."

"Because these systems are so unpredictable we've got to treat every part of that area as though it could be hit by a low grade cyclone in the next 48 hours."

Tupper said the cyclone predicted for the Northern Territory coast areas will not be anything like the destructive Cyclone Yasi in Queensland.

Heavy rain and strong winds have already forced the closure of the Botanic Gardens and Territory Wildlife Park.

The operators of the Mandorah ferry also said strong winds and heavy seas have prevented the ferry from running on Tuesday.

Also, due to the tropical low sitting over the north of the Darwin Daly district, Darwin is currently experiencing heavy rainfalls.