"We have evacuated at least 100,000 people from the Bhandara and Gondia districts of Maharashtra's Vidharba region since yesterday," state information secretary Bushan Gagrani said on Friday.
He said 200 villages in these two districts were "encircled" by water released from the nearby Raju Sagar dam in neighbouring Madhya Pradesh state.
The Maharashtra state government had on Thursday issued a high alert covering these districts, about 400km from India's financial capital Mumbai.
"The alert issued yesterday still remains," Gagrani said.
More than 1000 people died in August after record monsoon rains caused widespread flooding and massive water damage to Mumbai.
The region has again been lashed by heavy rains over the past three days, but no deaths have been reported so far during the latest alert.
The army and navy have been called in to aid rescue and rehabilitation operations.
"The rescue work is still on, and soon we will start on relief measures," Gagrani said.
State chief minister Vilasrao Deshmukh was expected to visit the flood-hit areas Friday, officials said.