More than 1,700 people have been arrested since police began raiding the homes of Pakistan Tehreek-e-Insaf supporters on Monday night, said Interior Minister Rana Sanaullah, who previously accused protesters of planning to carry weapons.
Islamabad's entry and exit routes have been blocked, as well as important civic sites, officials said. Entry and exit points were also blocked to and from all major cities in Punjab province and on the Grand Trunk Road (GTR).
Since being removed from power through a no-confidence vote last month, cricket star turned politician Khan has heaped pressure on the country's fragile new coalition rulers by staging rallies, touting a claim he was ousted from office in a "foreign conspiracy".
He was brought down by opposition parties in part by his failure to rectify the country's dire economic situation, including its crippling debt, shrinking foreign currency reserves and soaring inflation.
The government headed by Prime Minister Shehbaz Sharif had pledged to stop the protesters from entering the capital, calling the rally an attempt to "divide the nation and promote chaos".
"We will remain in Islamabad till the announcement of dates for dissolution of assemblies & elections are given," Khan later tweeted.
Khan's supporters also clashed with security forces in other major cities, including the southern port city of Karachi and the eastern city of Lahore.
Pakistan's Supreme Court, later in the day, ordered the government and Khan's party to negotiate on holding a peaceful public meeting in Islamabad.
File Photo: A police vehicle dispersing PTI protesters in Rawalpindi, Pakistan.