He has also been wounded by defections from his ruling Pakistan Tehreek-e-Insaf (PTI) party.
“The prime minister is as good as gone,” the influential English-language Dawn newspaper said in an editorial on the front page of its website.
Mr Khan took power in 2018 vowing a new Pakistan where he would purge the dynastic political elite responsible for the the country’s entrenched corruption.
His promises attracted a fervent following among the country’s young and middle classes. But analysts and his opponents said he also benefited from the backing of the country’s powerful generals who have long wielded influence behind the political stage and had fallen out with the former government. Mr Khan has denied having the backing of the military and the generals maintain that they do not meddle in politics.
Once in power, Mr Khan inherited a worsening economy and continued to wrestle with high inflation and a balance of payments crisis, wreaking havoc on the living standards of his supporters.
He has also appeared to clash in recent months with the all-important military, including a disagreement over the appointment of a new military spy chief.
Mr Khan has in recent days cast the challenge against him as a scheme by unnamed foreign powers who want him out because of his refusal to kowtow to them on foreign policy.
His removal would set off a new round of political instability in the nuclear-armed nation of more than 220m which has been ruled directly by the military for much of the time since independence.