Mr Gopalaswami has reportedly complained against a colleague
India's law minister has criticised the head of the election commission for behaving like a "political boss".
Minister Hans Raj Bharadwaj's comments came after election chief N Gopalaswami accused his colleague Navin Chawla of "bias" and recommended his removal.
Mr Bharadwaj advised Mr Gopalaswami to "prepare electoral rolls and not to settle scores".
The spat has created a controversy with general elections due in India in a few months' time.
Analysts say the ongoing row is a serious development as India's highest election body has been conducting elections successfully and has been considered non-partisan in its conduct.
"Gopalaswami should do his work in EC (election commission) and not become a political boss," Mr Bharadwaj told reporters in the capital, Delhi.
Mr Gopalaswami has defended his position, saying he was within his constitutional right to seek Mr Chawla's removal.
"In my mind, I am right," the Press Trust of India news agency quoted him as saying.
Reports say Mr Gopalaswami has written to the president of India seeking the removal of Mr Chawla, accusing him of "bias".
Over a year ago, the opposition Bharatiya Janata Party (BJP)-led National Democratic Alliance (NDA) lodged a complaint with Mr Gopalaswami seeking Mr Chawla's removal.
Senior BJP leaders have accused Mr Chawla of being biased towards the governing Congress party.
Mr Chawla denies the charge and has refused to quit.
The Congress has also denied the allegation against Mr Chawla, and criticised the opposition BJP for an "irresponsible and short-sighted assault" on the election commission.
"It is contrary to established law, hypocritical and duplicitous in terms of sequence and timing and totally distorts context and background," Congress spokesman Abhishek Manu Singhvi said.
General elections are due in India in April-May.
India's election commission is a three-member organisation and is headed by the chief election commissioner.
Mr Gopalaswami's term as the commission's head ends on 20 April.