Pakistan had given migrants without proper papers until November 1 to leave the country voluntarilyor face arrest or expulsion. The vast majority of undocumented foreign citizens in Pakistan are Afghans.
Islamabad has blamed Afghans in Pakistan for smuggling, terror attacks and petty crimes.
What do we know about the Afghans leaving Pakistan?
Before the announcement, around 1.7 million Afghan refugees were living in the country. Many Afghan citizens have lived in Pakistan for decades, having fled the neighboring country amid years of conflict.
Reuters news agency cited Khyber Tribal District Deputy Commissioner Nasir Khan as saying that more than 24,000 Afghans left Pakistan through the Torkham border crossing on Wednesday.
Officials told the German DPA news agency at least 30,000 Afghans had fled Pakistan over the last 24 hours.
"We expect a similar number of people would cross the border today," Fazal Rabbi, deputy head of Pakistan's agency for refugees, told dpa.
Over 140,000 refugees had crossed into Afghanistan before the November 1 deadline, according to Pakistani government statistics.
Major international aid agencies warned of chaotic scenes as people returned to Afghanistan.
Aid organizations warn of 'dire' conditions
Three aid organizations, the Norwegian Refugee Council, the Danish Refugee Council and the International Rescue Committee, said many people fleeing Pakistan's crackdown on irregular migration arrived in Afghanistan in poor condition.
"The conditions in which they arrive in Afghanistan are dire, with many having endured arduous journeys spanning several days, exposed to the elements, and often forced to part with their possessions in exchange for transportation," the agencies said in a joint statement.
The agencies said they feared for people's survival and reintegration into Afghan society, which has grappled with a humanitarian crisis sparked by decades of war, a struggling economy, and natural disasters.
Afghanistan's Taliban rulers have also denounced the deportation order as "cruel and barbaric," urging Pakistan to give undocumented Afghans in Pakistan more time to leave. The Taliban have prepared temporary camps for Afghans in border areas.
Islamabad's deportation plans have been criticized by the United Nations and Western embassies, who have urged Pakistan to develop ways to protect Afghans facing the risk of persecution under the Taliban.
sdi/sms (Reuters, dpa, AP)