As polls closed, Election Commission spokesman Nadeem Qasim said that the commission had told Khan that his vote could be disqualified because he cast his ballot in front of TV cameras, violating constitutional provisions on "the secrecy of the ballot paper".
He told reporters on Wednesday night election results were coming in later than expected because of issues with the "transmission system".
The PML-N, on the other hand, says it is the target of the alleged military machinations, with candidates under pressure and Nawaz Sharif ousted from power a year ago and jailed over a corruption conviction days before the vote, removing Khan's most unsafe foe from the race.
The vote is proving to be a close fight between Khan's Pakistan Tehreek-e-Insaf (PTI) party and the Pakistan Muslim League-Nawaz (PML-N), led by jailed former Prime Minister Nawaz Sharif. Results will start trickling in within hours, and the likely victor should be known by early Thursday.
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The third largest party in the running is the left-leaning Pakistan People's Party, headed by Bilawal Bhutto, the son of late Prime Minister Benazir Bhutto, who was assassinated by the Pakistani Taliban, whom she had vowed to eradicate.
The most populous province of Punjab - which has 141 out of the 272 directly elected seats in the National Assembly - is a key battleground, analysts have said.
The polling for the general elections across Pakistan started at 8 am which will continue till 6 pm without any formal break.
The Election Commission of Pakistan will release the results by constituency, as well as projections and votes polled for the candidates on each seat.
"We support free, fair, transparent and accountable elections in Pakistan, as we do around the world; and we encourage all Pakistanis to peacefully exercise their democratic right to vote", the spokesperson said.More news: Donald Trump to Iran President
The election results will also come in live on the official Pakistan election website: www.ecp.gov.pk but the site was down Wednesday evening.
At least 31 people were killed in a suicide bombing outside a polling station in the southwestern Baluchistan province. The Imran Khan-led Pakistan Tehreek-e-Insaf (PTI) has claimed victory despite serious questions being raised over the authenticity of the election process. PML-N's Amir Muqam is leading in NA-29 constituency.
"This is a deplorable and cowardly attack on a day when voters across Pakistan should be casting their ballots in a peaceful environment, without fear or hindrance", Michael Gahler, the EU's chief observer to Pakistan, said.
Khan has been an outspoken critic of the US-led war in neighbouring Afghanistan as well as China's massive investment in Pakistan, which has racked up millions of dollars in debt to Beijing.
In the ongoing elections, as many as 105.96 million people, including 47 million female voters, will be able to use their right to vote, with over 1,2000 candidates vying for 270 national and 570 provincial assembly seats.More news: Senators push sanctions to send Putin election meddling warning
"Past history suggests those daring enough to try and chart a more independent course or assert some degree of civilian control over the military are quickly discarded and emasculated by Rawalpindi, which inevitably finds a new political host to co-opt", Smith said.
A political party has to secure at least 172 seats to form the government in the 342-seat National Assembly. "We know all the other candidates and parties".
"If there are certain polling stations where they have any complaints, we should be approached".More news: Stocks end slightly lower as traders shrug off trade talk
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