Thackeray has opposed the diversion of Upper Wardha irrigation project water for the project. On Sunday night, 15 unidentified persons had hurled stones at the Indiabulls Finance Centre in Mumbai.
The MNS chief has accused deputy chief minister Ajit Pawar, who holds the energy portfolio, of diverting irrigation water to Indiabulls' power plant.
An Indiabulls employee at Amravati said windows and other valuable articles of the office were damaged in stone pelting.
"There were seven persons including two women. We are looking for them," said Ajit Patil, commissioner of police, Amravati city.
The company had signed an agreement with the state government in May 2011 to get water for its project from the Upper Wardha Irrigation Project.
An NGO, however, filed a public interest litigation in the Nagpur bench of Bombay HC, claiming the diversion of water was in violation of the governor's directives on usage of funds for backward regions.