Two cars went missing on Christmas Day while driving between Kiwirrkurra and Kintore, across the Western Australian and Northern Territory borders, police said at a press conference on Tuesday.
Two adults and a young child were in the first car while the second contained three people. They never arrived at their location.
Northern Territory Duty Superintendent Brendan Muldoon said they are "seriously concerned for their welfare."
Another missing man, an Asian tourist, was found on Tuesday afternoon after his car plunged into the Hugh River, 25 miles south of Alice Springs.
He was washed off a causeway into the Hugh River, rolling a few times before wedging in a tree. While the driver and one passenger escaped, the missing man failed to get out.
Late in the afternoon police announced he had been found with minor injuries.
Eight times average rainfall
The unusually heavy rainfall in normally arid central Australia was caused by low-pressure trough, which was swept in from the west coast of the country, Australia's Bureau of Meteorology forecaster Sally Cutter told CNN.
"Basically when these tropical lows move inland they can dump a huge lot of water, and that's what happened in this case," she said. "It just maintained its structure when it moved inland."
Just over 9 inches (231.6 millimeters) of rain fell in Kintore, Northern Territory, in less than 24 hours -- more than five times their monthly average.
Flood waters as high as one meter (3.3 feet) caused evacuations in the small town of less than 500 people, police said, as homes were inundated with water.
Heavy falls are so rare in this area, there are only a few rain gauges to measure it, Cutter said.
Photos of rain waters streaming off Australia's iconic Uluru went viral around the world in the days after Christmas.