Veranasi goes to the polls on Monday, the final day of India's mammoth general election, and results are due next Friday.
"With full responsibility, I'm accusing India's election commission of discrimination," Mr Modi told supporters at another rally in the electorally crucial state of Uttar Pradesh, where one in every six Indian voters lives.
The independent monitoring agency is widely credited for ensuring free and fair elections in India, in which 815 million voters have been called to the polls over five weeks.
The election commission's head, VS Sampath, rejected Mr Modi's allegation, saying it was determined to act impartially and was not afraid of any political party.
Certain parties were making "harsh and sweeping allegations" against the agency, Mr Sampath said.
Polls show Modi's Hindu nationalist Bharatiya Janata Party (BJP) winning the most seats in the election, although it may need to recruit allies to secure a parliamentary majority.
The party has grown increasingly critical of the election commission as campaign efforts are funnelled into the seats still up for grabs, accusing it of being partial and not deploying enough central security forces at polling booths.
BJP leaders wearing orange caps emblazoned with "Modi for PM" logos held protests both in Varanasi and the capital New Delhi, alleging the agency was blocking Mr Modi from campaigning in Varanasi.
The commission said police had raised security concerns regarding Mr Modi's rally which it could not ignore.