Under the new Pakistani government, Ghaffar Khan was under house arrest without charge from 1948 till 1954. Released from prison he gave a speech again on the floor of the constituent assembly, this time condemning the massacre of his supporters at Babra Sharif.
"I had to go to prison many a time in the days of the Britishers. Although we were at loggerheads with them, yet their treatment was to some extent tolerant and polite. But the treatment which was meted out to me in this Islamic state of ours was such that I would not even like to mention it to you." Badshah Khan, Budget session of Assembly on March 20th, 1954."
He went on to say:
"Six years ago, I announced on the floor of this House that Pakistan is our country and its solidarity and protection is our duty and that any program that will be submitted by any party for its progress and its reconstruction shall have my fullest cooperation. I repeat those words of mind even today. But still there are some persons who suspect my loyalty. I therefore think that it would be advisable to set up a tribunal to enquire not only into the question of loyalty or treason but also into the general massacre, arson and loot and the dishonouring of women and children and old men at Charsadda and the oppressive treatment meted out to us in jail." Badshah Khan, Budget session of Assembly on March 20, 1954.
Despite his vitriol he confounded his opponents and Indian supporters, who had long agitated for Ghaffar Khan's release, when to cheering crowds he supported Pakistan's claim to the disputed territory of Kashmir and went on to claim that he had twice offered his services in Kashmir on Pakistan's behalf.[3]
Re-arrested in 1956 or his opposition to the One-Unit scheme he remained in prison till 1959. Upon being released he went into exile in Kabul. In 1969, he was invited to India to attend the 100th birthday of Gandhi, his first visit after independence.
In 1962, Abdul Ghaffar Khan was named an "Amnesty International Prisoner of the Year." Amnesty's statement about him said, "His example symbolizes the suffering of upward of a million people all over the world who are in prison for their conscience."
His autobiography My life and struggle: Autobiography of Badshah Khan was published in 1969.
He visited India and participated in the centenary celebrations of the Indian National Congress in 1985; he was awarded the Bharat Ratna, India's highest civilian award, in 1987.
Ghaffar Khan died in Peshawar under house arrest in 1988 and was buried in Jalalabad according to his wishes. Although he had been repeatedly imprisoned and persecuted, tens of thousands of mourners attended his funeral, marching through the historic Khyber Pass from Peshawar to Jalalabad. A cease fire was announced in the Afghan Civil War to allow the funeral to take place, even though it was marred by bomb explosions kllling 15.[4]
"Better be poisoned in one's own blood then to be poisoned in one's principle."
His eldest son Ghani Khan was a poet. Another son Khan Wali Khan is the founder and leader of the Awami National Party and was the Leader of the Opposition in the Pakistan National Assembly. His third son Ali Khan was non-political and a distinguished educator, and served as Vice-Chancellor of University of Peshawar. Ali Khan was also the head of Aitchison College, Lahore, and Fazle Haq college, Mardan.