A magisterial inquiry had been ordered into the firing, District Collector Vikas Deshmukh said.
He clarified that the death toll in the police firing so far was three and not four as reported earlier and one of the seriously injured was being treated at a hospital at Talegaon.
Mr Deshmukh said about 50 police personnel including 10 officers were injured in the stone pelting during the protest on the Mumbai-Pune Expressway.
Farmers were protesting a pipeline project on the Pavna dam to facilitate water supply to the industrial township of Pimpri-Chinchwad due to which their agricultural water supply would be severly affected.
Many private and police vehicles were damaged in the violence after the agitating farmers blocked the highway for hours on Tuesday morning.
Meanwhile, Maharashtra Deputy Chief Minister Ajit Pawar today visited the injured in hospitals to inquire about their condition.
Shiv Sena spokesperson and Member of the Legislative Council (MLC) Neelam Gorhe demanded Pawar's resignation, who is also Pune District Guardian Minister, for "unwarranted" police firing at Maval.