Christians are among hundreds of thousands of Afghan refugees that Pakistan was to begin forcibly repatriating on Tuesday (April 1) to Afghanistan, where the ruling Taliban has asserted they will kill any Christian, sources said.

There were more than 1.4 million registered and 700,000 unregistered Afghans in Pakistan, according Jude Simion of refugee aid group Philoi Global.

“These families face life-threatening dangers because of their faith, ethnicity, nationality and political beliefs,” Simion said. “Deportation would expose them to extreme persecution under both the Pakistani and Afghan regimes.”

Many of the Afghan refugees had fled to Pakistan after the Islamic extremist Taliban returned to power in 2021. Concerned about Afghanistan harboring terrorist groups that have struck targets in Pakistan, and with international assistance for refugees dwindling due to freezes U.S. President Trump ordered on Jan. 20, Pakistan reacted quickly. In February officials announced that after March 31 Pakistan would repatriate at least 44,000 Afghans awaiting resettlement in Western countries, more than 800,000 holders of Afghan Citizenship Cards and an unknown number of undocumented Afghan migrants.

More than 20,000 Afghan refugees and their families were awaiting resettlement in the U.S. under special immigrant visas for assisting U.S. and NATO forces, but President Trump’s order paused all refugee resettlement in the United States except for individual cases – a process requiring time that refugees no longer have.

A decline in international assistance was a key factor in Pakistan’s decision to increase deportations, a senior Pakistani diplomat told the Financial Times on condition of anonymity. Before Trump’s order froze nearly all foreign aid, including refugee assistance programs, the U.S. last year accounted for 42 per cent of more than $100 million in international aid Pakistan received for Afghan refugees, FT reported, citing the U.N. High Commissioner for Refugees.

For Afghan refugees in the key cities of Rawalpindi and Islamabad, the Pakistani Prime Minister’s Office on Jan. 29 issued a circular ordering the immediate repatriation of Afghans with Afghan Citizen Cards and Pakistan Origin Cards, Simion of Philoi Global said.

“These documents were meant to offer some protection, but now they are used to identify and deport vulnerable individuals,” he said.

One Afghan without a visa told a Philoi Global worker that he did not know what he would do after March 31.

“The Taliban will definitely will kill me,” the refugee said. “The main reasons are as I am Christian, and I worked with the previous government of Afghanistan as a military person.”

Another Afghan refugee asked a Philoi Global worker to pray for renewal of his visa.

“The situation here has become really terrible, especially for those who are alone,” he said. “No one lends a helping hand because I am single. If I cannot renew my visa, I will be forcibly deported, and I will be destroyed by the Taliban terrorist group, please pray in the name of the Holy Spirit on this matter.”

Nearly 1,660 Afghans had been cleared for resettlement in the United States before Trump’s order suspended refugee programs, and their flights were canceled, Simion said. Germany had deported at least 28 Afghan asylum seekers late last year, he said, adding, “We are observing increased pressure from right-wing parties, which are gaining influence in governments and advocating for the deportation of Afghans.”

Iran has already indicated plans to send back Afghan refugees, and neighboring countries have begun deporting Afghans as well, Simion said.

The Taliban have said they will kill any Christians and have gone door-to-door to find them, according to Open Door’s 2025 World Watch List report.

“Afghan church leaders were specifically targeted; many have disappeared, while others have been beaten, tortured and killed,” the report stated. “Any existing house churches remain deeply underground, and Christians live under relentless pressure. If converts from Islam are discovered, the family, clan or tribe may try to preserve its so-called ‘honor’ and oppose the convert through pressure, violence or even murder.”

One of Afghanistan’s General Intelligence directorates last month raised specious accusations that some Shia Muslims had become Christians and ordered their arrest, according to the Afganistan Women’s Voice advocacy group.

In an order to intelligence directors in Daikundi and Bamyan directorates, the head of Directorate 376, which focuses on counterintelligence and secret policing, ordered the arrests of “a number of Shiite youths” who had served in the previous government.

“Now, in order to work for Jesus, they have been given privileges and plans by European countries,” the director, identified only as Dr. Bashir, stated in the order. “Therefore, the matter as it was, was shared for your understanding. Investigate and investigate in the field, and by stabilizing the issue, catch the perpetrators.”

In a Facebook post, the Afghanistan Women’s Voice called the accusations a pretext to defame and suppress young Hazaras, one of Afghanistan’s largest tribes.

“Now it remains to be seen how many Hazara youth are arrested for the crime of [supposedly being] ‘Christian missionaries’ by adhering to this letter,” the group stated. “It is evident that the name of Christianity has not even been mentioned among the youth of Daikundi in Bamiyan, let alone to promote it.”

Shia Muslims make up an estimated 10 to 15 percent of the country’s nearly entirely Muslim population.