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"The decision reflects Pakistan's continued efforts for facilitating Afghan transit and trade. This is not a pedestrian crossing, but is meant for facilitation of trade and transit vehicles," The Nation daily quoted the ministry as saying on Saturday.
Two major crossings - Torkham and Chaman - were already opened earlier.
Government sources said the decision to open the Kharlachi crossing for trade was part of the confidence-building measures of Islamabad to make Afghanistan realise that Pakistan wanted to see stability in the country.
During a meeting with Afghan President Ashraf Ghani on the sidelines of the SCO summit last week, Prime Minister Nawaz Sharif had reiterated his commitment to support the Kabul government in bringing peace to the country, reports The Nation.
In February, Pakistan completely sealed the border crossing with Kabul for over a month after the attacks.