Agreeing with the NGO's plea, the bench passed the path-breaking verdict and introduced the concept of negative voting in the election process, saying that it would further empower the voters in exercising their franchise.
The latest verdict is part of series of judgements passed by the apex court on the election process.
Earlier, the apex court had restrained people in custody from contesting elections.
The apex court has also ruled that MPs and MLAs would stand disqualified after being convicted of serious crimes.
The government has brought an ordinance seeking to negate the court's judgement striking down a provision in the electoral law that protected convicted lawmakers from immediate disqualification.
A two-judge bench of the apex court had felt that the issue on negative voting needed to be adjudicated by a larger bench as there were certain doubts over the interpretation of the ruling passed by a Constitution Bench in the Kuldip Nayar Vs Union of India case relating to a voter's right.
Under the existing provisions of Section 49(O) of the Representation of People Act, a voter who after coming to a polling booth does not want to cast his vote, has to inform the presiding officer of his intention not to vote, who in turn would make an entry in the relevant rule book after taking the signature of the said elector.
According to the PUCL, Section 49(O) was violative of the constitutional provisions guaranteed under Article 19(1)(a) (Freedom of Speech and Expression) and Article 21 (Right to Liberty) and violated the concept of secret ballot.