The alert was issued at 6.44am (local time) and warned people in or near Bidyadanga to Sandfire including Bidyadanga to look for shelter immediately.
The Department of Fire and Emergency Services (DFES) said there was a threat to lives and homes, and people were in danger and needed to act immediately.
A yellow alert remained in place for people between Broome and Pardoo Roadhouse.
The category two cyclone was crossing the far west Kimberley coast near Anna Plains, moving east at 9km/h.
The Bureau of Meteorology (BOM) upgraded the cyclone to a category two, on a scale of one to five, as it approached the Australian coast between Sandfire and Bidyadanga, bringing furious winds of up to 150 kilometres per hour near the centre of the storm.
Devastating gales of 100kph are possible in remaining areas between Bidyadanga to Wallal Downs.
Relentless rainfall is likely to continue over the west Kimberley and far east Pilbara throughout the day.
The rain has forced the closure of parts of the Great Northern Highway, which links Western Australia’s capital city Perth with its northernmost port, Wyndham.
Main Roads regional manager Andrew Pyke said the heavy rains could end up closing major roads and highways after the area already had major rainfall.
He said crews were closely monitoring the situation but there were fears conditions could get worse.
Mr Pyke added: “We’ve got a lot of water sitting on the Roebuck plains area now and a lot of water happened in the last 24-48 hours in the Broome area, and there is more water coming down with the passing of this cyclone.
“It is quite difficult. There have certainly been significant damages of some roads in the Kimberley with the water that’s flowed over the roads. We are very concerned.”
The storm, which was upgraded from a tropical low to a cyclone yesterday afternoon, was initially forecast to develop into a category three storm, however, it weakened on its way towards the Kimberley coast.
Andrew Burton, a senior forecaster at the Bureau of Meteorology’s tropical cyclone centre, said the Kimberley and Pilbara could expect a drenching.
He said: ”I think we’ve already seen one of the strongest impacts of this system that Tropical Cyclone Kelvin will have — [that] is the rainfall we’ve seen in Broome.
“We’ve had 370.6 millimetres up to 9:00am [Saturday] and that rainfall is continuing, so they look like they’re on track to get to their wettest year ever.”
The town of Broome has already recorded almost 90mm over the last 24 hours.
Cyclone Kelvin is expected to weaken later Sunday as it moves inland.