The Chaman border crossing at the Pak-Afghan border was closed Wednesday evening for an indefinite period.
The crossing points on the border had opened on March 7 and 8 following instructions from the federal government.
"The border has been closed for an indefinite period,” said a Federal Investigation Agency (FIA) official.
The official added that only valid passport holders were allowed to cross the border into Pakistan.
Thousands of Afghans crossed the Friendship Gate at Chaman and entered Afghanistan. The official said “some Afghan families are entering their country”.
Long queues of people were witnessed on both sides of the border. Women and children were also among those crossing the border, the FIA official added.
Hundreds of trucks loaded with Afghan transit goods were also parked at the border, with 200 empty trucks standing on the Afghan side waiting to enter Pakistan, said the former president of chamber of commerce Chaman, Engineer Daro Khan Achakzai.
Earlier this week, Pakistan had temporarily opened border crossings at Torkham and Chaman for two days to allow stranded Afghan nationals to return to their country.
Ministry of Foreign Affairs said the government decided to open the border crossings on Tuesday and Wednesday, March 7 and 8, "in order to provide an opportunity to those nationals of Afghanistan who had come to Pakistan on valid visas and wish to return to their country."
The government had decided to seal the border crossings for an indefinite period on February 16, in the aftermath of a suicide attack at the shrine of Lal Shahbaz Qalandar which killed 90.
The border was ordered closed for all kinds of communication due to 'security concerns'.