Some papers have also published speeches by Taliban insurgency leaders, he added, at a time when the government is trying to lure the Taliban into nascent peace talks aimed at ending the 11-year Afghan war.
"We totally reject these statements and the ban is to show them this," said Taheri, adding the nation-wide ban could only be reversed by a ministerial decree.
Afghan border police have been ordered to sweep shops in the eastern provinces of Nuristan, Kunar and Nangarhar near the Pakistan border to seize copies of Pakistani papers, he said.
The eastern area has been a focus for foreign and Afghan security operations against insurgents over the summer months ahead of a NATO pullout of most combat troops by 2014.
Ties between Afghanistan and Pakistan have been strained by months of cross-border shelling which officials in Kabul have blamed on Pakistan's military. Islamabad accuses Afghanistan of failing to stop anti-government militants operating from mountain havens on Kabul's side of the border.
On Thursday, the Afghan foreign minister told the UN Security Council in New York that diplomatic ties with Pakistan were under threat.