Their predicted margin of victory is larger than surveys indicated in the run-up to the vote when most polls showed the NDA would be the largest alliance but would fall short of an overall majority.
Counting of votes began at 08:00 am and trends are expected to be known by noon because of the use of computerised voting machines. Final results in the polls, in which around 900 million Indians were eligible to vote, are due by the evening.
The voting was held in seven phases with first phase beginning from April 11.
The last phase of voting was held on May 19. Over 67.11 crore voters exercised their right to vote.
The NDA held a meeting on Tuesday, at which Modi was garlanded with flowers by members of the alliance, to discuss its policy agenda for its second term in power. It has promised to double farmers' income and boost infrastructure spending over the next five years.
"Do not get demoralised by the fake exit polls doing the rounds," Congress president Rahul Gandhi said in a message to party workers posted on social media on Wednesday.
The opposition alliance has also protested to India's Election Commission over the electronic voting machines (EVMs) used in the count, that they alleged can be tampered with, and requested a delay to counting while votes are tallied with a backup paper audit trail.
The commission rejected the opposition's demands on Wednesday.
Around 500 masked people carrying guns and machetes attacked a polling team and forcibly took away EVMs in the remote northeastern Indian state of Arunachal Pradesh, Reuters reported on Wednesday, though elections in the country as a whole are widely considered to be free and fair by international observers.