Pakistan is the main source of goods and food supplies for landlocked, impoverished Afghanistan.
In Afghanistan, Abidullah Uqab, a spokesperson for the border police, confirmed that all the border crossings with Pakistan remained shut for trade and movement of people on Monday.
It was not clear when the border might reopen.
Though the Chaman border crossing was closed for trade, authorities briefly allowed about 1,500 Afghan nationals stranded there since Sunday to return home on foot, government officer Imtiaz Ali said.
Torkham, however, remained closed to all travel and trade. The closure was confirmed by Mujib Ullah, a representative for local traders.
Afghan refugees, including many who were waiting to leave Pakistan because of a crackdown on foreigners living in the country illegally, said they had been waiting at the Torkham crossing since Sunday.
Gul Rahman, a refugee, said he waited through Sunday at Torkham before returning with his family to the northwestern city of Peshawar.