The death toll from Malaysia's disastrous floods has risen to 12, with another youth missing, but authorities said fears of another round of flooding had been averted.

The latest confirmed victim is a five-year-old girl whose body was found late Friday, the official Bernama news agency said.

She was swept away when the car her family was travelling in was caught by strong currents. Her father survived, but her mother and three-year-old sister also died.

However, an 18-year-old youth is missing after he was lost in floodwaters late Friday, Bernama said.

Malaysia's opposition has called for an inquiry into the floods, the worst in decades, which have forced nearly 59,0000 people in southern Johor state to flee their homes and take shelter in relief centres.

However, Johor chief minister Abdul Ghani Othman said he was confident the situation in the state would be back to normal within the next few days.

Abdul Ghani said the second wave of rains predicted by forecasters would not take place as the rain-bearing clouds had been blown towards Singapore and Sabah state on Borneo island.