State Disaster Management Authority sources said that the 40 villages were in Dhemaji, Chrang, Sibsagar, Bongaingaon, Jorhat and Lakhimpur districts.
It said that in Bongaigaon district 20,000 people were hit in 22 villages.
The 60 dwellings destroyed in Morigaon district were situated between Goroimari and Bhajaikhaity villages under the Lahorighat revenue circle in the riverine 'Leoramukh' area, the sources said.
The affected families were sheltering on the river embankment, the sources said.
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The Bramhaputra was flowing one metre above danger level in Morigaon district, they said.
Besides, over 100 villages in Dhemaji, Chirang, Jorhat, Lakhimpur and Sivasagar districts were under flood waters.
Altogether 3500 people were sheltering in 11 relief camps in Dhemaji, Chirang and Sivasagar districts.
The first wave of floods since mid-May has affected nearly 1.5 lakh people in about 500 villages across 12 districts in the state.
The flood has so far claimed one human life in Morigaon district.
It has also hit the Kaziranga National Park and Pobitora Wildlife Sanctuary with an elephant and an antelope perishing in Nagaon district.