Khan, who heads the Pakistan Tehrik-e-Insaf party, said it should be the country's state policy to ensure that there are no militant groups operating from within Pakistan.
He remarked that as things stand today, Pakistan has no choice but to go this way.
"As a policy, if the Pakistan Tehrik-e-Insaf government comes to power, we will insist on there being no militant groups operating within Pakistan because the world has changed. The groups were created during the Afghan jihad, and this is now an outdated concept of having them as assets," Khan said in an interview to Karan Thapar for CNN-IBN's Devil's Advocate programme.
However, when he was specifically asked if he would check the activities of Saeed, who masterminded the 2008 Mumbai attacks, along with his group JuD and its front organisations like the Falah-e-Insaniyat Foundation, Khan did not commit himself to acting against these elements due to perceived fears posed by extremists.
"Look, I'm living in Pakistan. Pakistan at the moment is the most polarised country in the world. A Governor gets shot, his assassin becomes a hero.There's no point in becoming a hero right now in this country where there's no rule of law," he said, referring to the assassination of Punjab Governor Salmaan Taseer.
"Life is very cheap here, so just let me make a policy statement. Don't just go into details. As a policy statement, it should answer your question. No militant groups (will be) operating from within Pakistan," he said.
Taseer, a top leader of the ruling PPP, was gunned down by a police commando who was part of his security detail outside a restaurant in Islamabad in January.
Mumtaz Qadri, the policeman who killed the Governor, said he was angered by Taseer's criticism of the controversial blasphemy law. Qadri was subsequently convicted and sentenced to death by an anti-terrorism court.
However, hardline religious and extremist groups and even lawyers' organisations hailed him as a hero and demanded that the President should pardon him.
During the interview, Khan said the time had come to not only remove all militant groups (and) disarm them but also to work for the de-weaponisation in Pakistan because it is causing massive problems within the country.
"Therefore, once that issue disappears, once there are no militant groups within Pakistan, I think that issue will disappear," he contended.
Asked how his party's policy towards India would be different, Khan replied that he would work for a new relationship based on mutual trust in which intelligence agencies would have no role.
He said, "At the moment, Pakistan doesn't trust India. India doesn't trust Pakistan. Here there is a big perception that our water is being stolen, and (in) Balochistan, the Indian secret services are active with the BLA (Balochistan Liberation Army). In India, the perception is that any terrorist act is financed by Pakistan's ISI.
"You can never have a relationship based on mistrust. I think the time has come to have a new relationship and I believe that if you can eliminate the roles of intelligence agencies, (the) two civilian governments can sit together and say we'll resolve all our issues through dialogue. I think it's the way forward because the benefits of peace are enormous," he added.