Foreign Office spokesperson Mohammad Faisal said that elections are a part of the democratic process and the Indian media must focus on its internal matters. He said the tallying was now being conducted manually. The results had been due by around 2 a.m. (2100 GMT on Wednesday).
Analysts said investors were relieved Khan was unlikely to have to rely on major opposition parties in a messy coalition.
The uncertainty of the outcome of the vote - no single party appeared assured of a simple majority win - could also lead to prolonged post-election jockeying that would hamper the forming of the next government.
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, assassinated by the Pakistani Taliban, whom she had vowed to eradicate. The PPP was leading in races for 42 seats.
More than a dozen TV channels in Pakistan, based on official but partial counts, are projecting that Khan's Pakistan Tehreek-e-Insaf party is getting as many as 119 seats of the 270 National Assembly seats that were contested. According to PTV news, Imran Khan has maintained a massive lead over PML-N's Shahid Khaqan Abbasi in Islamabad constituency.
Supporters of Pakistani politician Imran Khan. As 70% population in Pakistan is under 30, the demagogue has garnered the support of many young voters.
In contrast to the PML-N, Khan is also against China's huge investment in Pakistan, which has racked up billions of dollars in debt to Beijing.
Such a delay could further imperil Pakistan's economy, with a looming currency crisis expected to force the new government to turn to the International Monetary Fund for Pakistan's second bailout since 2013.
He is also widely believed to be backed by the army, which fell out with Nawaz Sharif, who looked to curb the military's traditional dominance in politics.
At a midnight press conference when the vote count was underway, PML-N president Shahbaz Sharif said the election was a "blatant violation" of the mandate of the people.
Up to 800,000 police and military forces have been stationed at more than 85,000 polling stations across the country, with concerns for security after a string of bloody militant attacks in the final weeks of the campaign that have killed more than 180 people, including three candidates.
Islamic State claimed responsibility for that attack.
The Election Commission of Pakistan (ECP) denied the claims, saying a new electronic results system suffered unexpected glitches. Military dictators have ruled the country for half of the 71 years of its existence since its founding in 1947.
"These elections were 100 percent fair and transparent", said Chief Election Commissioner Sardar Muhammad Raza early Thursday as the outcry grew.
Babar Yaqoob, a top official at the Election Commission, said the turnout in Wednesday's vote was about 55 percent, slightly better than previous elections. The tweet featured a collage of pictures of Pakistanis handing military personnel at polling stations flowers and elderly women kissing soldiers.
Those and other allegations pointed to Pakistan's powerful military establishment.
Senator Mushahid Hussein, a central PML-N leader alleged that the Wednesday's elections were the "dirtiest" in the country's political history.
PML-N's campaign had been reinvigorated by the return to Pakistan of Nawaz Sharif, 68, who was earlier this month convicted and sentenced in absentia to 10 years in prison over the purchase of upscale London apartments using offshore companies in the mid-1990s.