Roads in the area too are damaged, district administration said.
Malin village in Ambegaon tehsil made global headlines in the monsoon of 2014 when a landslide flattened the hill-slope village, claiming 151 lives.
The government built new houses away from the original site which were handed over to villagers in April this year. However, with the first heavy downpour of the season, many houses developed cracks, locals said.
"Ambegaon region received a heavy rainfall yesterday. In 3-4 hours, rainfall was as high as 97 mm, which is rare in that area. With such heavy rains, we had anticipated some damage to houses and internal roads," said the district collector Saurabh Rao.
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The new houses were handed over in April this year in the presence of Maharashtra Chief Minister Devendra Fadnavis.
Rao further said, "We are expecting more damage because this is just the beginning of monsoon season. If there are more instances of such a heavy rainfall, there could be be more damage, but we will help the villagers."
A team of PWD, revenue department and Zilla Parishad officers is on the spot to assess the situation, Rao said.