The crossings at Torkham in Khyber tribal region and Chaman in Balochistan province were opened to let those with valid documents to cross over.
12,549 people crossed over to Afghanistan at Torkham while 470 entered Pakistan from the neighbouring country, The Express Tribune quoted officials as saying.
Another 6,848 Afghan citizens and 1,646 Pakistanis crossed back into their respective countries through the Friendship Gate at Chaman, a senior Federal Investigation Agency official said.
"But those without proper travel documents have not been allowed to cross over to either side (through Torkham)."
"We did not even entertain those Pakistani citizens who travelled to Afghanistan using only their identity cards," he said, adding that an alternative will be provided to them after authorities receive orders from the interior ministry.
However, those who crossed the border at Chaman were mainly Afghan and Pakistani traders travelling on special permits issued under an agreement signed between both countries' border authorities some months back.
Some 6,728 Afghans and 1,631 Pakistanis crossed the border at Chaman yesterday using the permits, officials said. Only 120 Afghans and 15 Pakistanis who used the crossing had visas, they said.
The Pakistan government had decided to close the border last month amid a string of deadly militant attacks, that killed more than 125 people, which the military claimed were carried out by militants operating from safe-havens in Afghanistan.
The two countries have long accused each other of failing to combat extremists who operate along their porous frontier.
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