The warning that storms and rainfall may occur till Friday was issued to allow the administration of the two states to prepare for any eventuality.
IMD's warning followed cyclonic storm and hailstones lashing Meghalaya in the past 36 hours, damaging hundreds of houses and other properties all over Meghalaya.
Over a hundred houses were damaged in several villages under Rongjeng C&RD Block in East Garo Hills yesterday, Deputy Commissioner Cyril Diengdoh said.
On Saturday, several houses were damaged especially in West Khasi Hills district as the storm hit several parts of the state.
Eighteen cows also died in a remote village in East Jaintia Hills district in a lightning strike on Friday.
A similar cyclonic storm lashed the state capital earlier this month and left at least seven persons injured.
Around 500 people were provided with shelter and food by the authorities as their houses were damaged in the storm.
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