Pakistani attempts to control the previously open border and implement customs duties have also sparked complaints from traders used to crossing with impunity.
Prime Minister Nawaz Sharif has announced the reopening of Pakistan's border with Afghanistan after a month-long closure due to rise in tensions between the two neighboring countries.
The Torkham and Chaman crossings are major arteries for $1.5bn in trade and commerce between the two neighbours.
Last month Pakistani military shelled a militant training camp on the Afghan side of the Durand Line.
The border closure, the worst since a two-week sealing in August, further undermines an already fragile relationship between the two countries, both of which accuse each other of harboring militant groups that carry out attacks.
He said the decision to re-open the border is being taken as a goodwill gesture.
Pakistan closed the border in mid-February following a string of deadly militant attacks which Islamabad has blamed on militants hiding in Afghanistan. Tensions along the frontier have been simmering for months, after hundreds of thousands of Afghan refugees in Pakistan were repatriated a year ago, with Human Rights Watch accusing Islamabad of coercion, threats and abuse.
In a statement, the Prime Minister said recent incidents of terrorism in Pakistan have been traced back to anti-Pakistan elements in Afghanistan.
In a temporary reprieve, Pakistan on March 6 reopened the main Torkhum and Chaman border points for two days, allowing thousands of stranded people to return home. Pakistan's Zakaria told reporters in Islamabad on Thursday while he can't give a date for reopening of the border, the measure is "temporary". "Pakistan shouldn't shut the lucrative crossings for the sake of a political issue".
The closure choked off a key trading route for landlocked Afghanistan. Afghanistan depends on Pakistani ports for its imports.