"Today is a historic and memorable day," Banerjee wrote on social networking site Facebook.
"The much-awaited transfer of chit-mahal enclaves between India and Bangladesh will be effected from today midnight," she added.
This June, India and Bangladesh ratified the Land Boundary Agreement that envisages the transfer of 111 enclaves with a total area of 17,160.63 acres to Bangladesh.
Under the agreement, Bangladesh will transfer 51 enclaves totalling 7,110.02 acres to India. There will be a 6.1 KM undefined border stretch demarcated.