Bhante Anand, President of the Akhil Bharatiya Bhikkhu Mahasangh (ABBM), an influential body of Buddhist monks, said, "We have information that the branch was sold to some Japanese for money in connivance with the temple management committee."
Anand added that he suspected involvement of international mafia.
He said there was a high demand of holy tree leaves, wood and soil of its root in Japan, where Buddhism has a large following.
Early on Friday Bihar Home Secretary Afzal Amanullah visited Bodh Gaya to inquire into the incident after the Prime Minister's Office sought a detailed report from the state government.
The tree behind the 1,500-year-old temple grew from the original banyan tree under which Buddha attained enlightenment. Buddhist pilgrims carry back leaves from the tree, believed to be the sixth regeneration of the original banyan tree.
The Mahabodhi temple was declared a World Heritage Site in 2002.