After the bill for formation of separate Telangana state was passed in the parliament in February, Rao had reportedly decided to quit the Congress and join the Telugu Desam Party (TDP).
However, the TDP leaders in West Godavari district opposed his admission into the party.
Rao has three decade old association with the Congress. He was first elected to Lok Sabha in 1984. He was again elected in 1989, 1998, 2004 and 2009.
He is the second central minister to quit over the state's bifurcation. Last month, D. Purandeswari had resigned as a minister and also quit the Congress. She joined the BJP.