Manikrao is currently a member of the Maharashtra Legislative Council and also elected as deputy chairperson of the house.He was previously a member of the Maharashtra Legislative Assembly from the Indian National Congress from 1985 till 2004. Manikrao has been a vocal critic of the Bharatiya Janata Party - Shiv Sena alliance government which ruled Maharashtra up to 1999, especially its handling of the Srikrishna Commission. On July 27, 1998, Manikrao along with R R Patil demanded that the Justice Shrikrishna Commission report be tabled on the floor of the assembly. This forced an adjournment of the assembly. His relentless criticism of the then government in the legislature ensured that when the government lost its mandate.
Manikrao was made minister of state in the home ministry of Maharashtra during 1992-1995 and again 1999-2003. As minister of state for home, he headed a committee that recommended police reforms such as time-bound promotions. He also admitted to the poor state of jails in the state.