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Hundreds of devotees, who had reached Ettumanoor temple the previous morning were not allowed to leave to Sabarimala citing the crowd of Erumeli and Pampa.
A yellow alert indicates rainfall ranging from 64.5 mm to 115.5 mm within 24 hours.
Michaung is expected to subside into a deep depression over the next six hours, said an official.
The relentless downpour, reminiscent of the 2015 deluge, paralysed daily life, prompting authorities to declare a public holiday on Tuesday.
The weather system is expected to persist till Thursday and thereafter become a deep depression and subside.
The rainfall deficiency in Idukki district is 54%.
'Michaung' and is likely to hit with a maximum sustained wind speed of 80-90 kmph gusting to 100 kmph, the IMD said.
Mosquitoes that carry viruses including dengue, malaria, West Nile, and Zika are shifting into new parts of the world as warmer temperatures and heavy rains create more hospitable conditions for them to breed.
Light to moderate rainfall will continue in the state from Thursday to Monday under the influence of a low-pressure area over the southwest Bay of Bengal.
The Met Department has predicted isolated heavy rains for four days from Friday.