In its order, the interior ministry said the newspapers “are a propaganda resource of the Taliban spokesmen” and has ordered police forces in east Afghanistan to confiscate all copies.
The latest move comes amid increasing tension between the two countries.
Afghanistan has urged Pakistan to immediately stop shelling in the border province of Kunar.
The Afghan interior ministry order focuses specifically on blocking entry of the papers at Torkham, a busy border crossing.
It authorises police to impound Pakistani newspapers in the three eastern provinces of Nangarhar, Kunar and Nuristan.
Referring to the reasons for the move, the ministry said news in the Pakistani newspapers “is not based in reality and it is creating concerns for our countrymen in the eastern provinces of Afghanistan”.
Correspondents say that cross-border violence has become a highly sensitive issue in Afghanistan, where many are wary of Pakistan’s historic ties to the Taliban.
At a UN Security Council meeting on Thursday, Afghan Foreign Minister Zalmai Rassoul said the attacks had killed dozens of civilians.
The UN says around 4,000 people have been displaced due to cross-border shelling.
Last month, Afghan President Hamid Karzai and his Pakistani counterpart, Asif Ali Zardari, agreed to send a joint military delegation to examine the shelling across their border.