Imran Khan, Pakistan’s prime minister, has appeared to drop his promise to grant citizenship to hundreds of thousands of Afghan refugees living on the margins of Pakistani society.

On Sunday Khan announced that he would start work immediately to provide passports to the children of refugees born in the country. However, after a backlash from politicians and supporters of the country’s powerful military, he said on Tuesday that no decision had been made.

About 2.7 million Afghan refugees have crossed the border into Pakistan since the Soviet invasion in 1979. Without official documentation they are shut out of schools and employment. As many as 1.5 million children born to refugees in Pakistan are denied citizenship.

After a strong push-back, Khan said he had raised refugee citizenship “just to initiate a debate”. The founder of the Pakistan Tehreek-e-Insaf (PTI) party, which swept to power in July, has a reputation for retracting his words.

However, Khan reiterated his own desire to grant citizenship to Bengali and Afghan refugees as he addressed parliament before leaving on a trip to Saudi Arabia and asked ministers for their suggestions on the issue.

“I will keep asking what will happen to these human beings … if we don’t decide on their rights now, when will we decide?” he said.

Parliament will offer stiff resistance, though. The PTI holds a slim majority and Khan’s announcement on Sunday was condemned by politicians in Pakistan’s Sindh and Balochistan provinces, who fear the impact of enfranchising new voters.

One of Khan’s key coalition partners, the army-supporting chief minister of Balochistan, Jam Kamal, said Pakistan should not alter its policy of seeking to send refugees home. The military has long called for repatriation of Afghan refugees, blaming them for terrorist attacks.

Local journalists, whose work is often censored to avoid displeasing the armed forces, said their stories on Khan’s original speech had not been published.

Hajji Abdullah Shah, head of the Afghan refugees in Sindh, told the Guardian he was anxious about the change in tone. “We hope he will not take the light, he has shown to us, back,” he said.

Mosharraf Zaidi, a columnist, while praising the sentiment behind Khan’s original offer as “really admirable” said the reversal was due to political inexperience and it was “quite upsetting”.

The prime minister was this month criticised for a U-turn on the appointment of Atif Mian, a world-leading economist, under pressure from Islamists who objected to his Ahmadi faith.