The latest round of floods come weeks after people had returned home from what Abdullah Badawi, the prime minister, described as Malaysia's worst flooding in a century.
At least 17 people have been killed in the two rounds of flooding.
Several relief centres in the hardest-hit Kota Tinggi area are overcrowded and cannot take in more evacuees, the Star newspaper reported - despite the government opening 39 new centres since the new flooding began on Thursday.
Güncelleme Tarihi: 20 Eylül 2018, 18:16
Many parts of Johor state lie in low-lying flat areas, making it susceptible to flooding from heavy rain.
Kota Tinggi was inundated on Saturday, when the Johor river's banks burst. Waters on Sunday rose to more than four metres, swallowing petrol stations and terrace houses, leaving only rooftops visible.
Batu Pahat has been the worst affected district with 31,376 people from 7,016 families sheltered at 116 relief centres.
|Batu Pahat's 116 relief centres are housing |
more than 31,000 evacuees [AFP]
The meteorological department said the heavy rain was expected to continue until Monday and issued a red alert warning.
The red alert is the highest of a three stage warning system and signals heavy monsoon rains and floods.
Abdullah has estimated the losses so far to be around 100 million ringgit ($28.5 m).