The National Directorate of Security (NDS) said the recent memorandum of understanding signed with Pakistan's Inter Services Intelligence (ISI) was not practical and that it will come under review by a panel of experts who will report directly to President Ashraf Ghani.
This comes after a major public outcry erupted last week following the signing of the accord, Afghan media reported.
In a statement issued by the NDS, the agency said that "in order to make the accord practical and to legitimise it a five-step process has been implemented".
This process includes, determine the framework, scope and authority of the agreement by President Ghani, refining the draft text agreement by experts from various government agencies. The team will report directly to the president.
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Further, discussions will be held on the draft agreement at a meeting of the National Security Council, Tolo news reported.
In the statement, the NDS said it is committed to putting the best interests of the country first in terms of considering such moves with foreign agencies.
Today's statement comes after the controversial MoU was signed about 10 days ago between the NDS and ISI committing them to "intelligence sharing and complimentary and coordinated intelligence operations."
After Pakistan Army spokesman broke the news of MoU, widespread public outcry ensued - with MPs, civil society activists, political parties and jihadi leaders all slamming the NDS-ISI accord.
Meanwhile, members of the security commission in the Wolesi Jirga (Lower House of Parliament) today summoned the NDS chief Rahmatullah Nabil to appear before them and answer questions, Khaama Press reported.
Pakistan and Afghanistan have long accused each other of sheltering Taliban militants, but ties have warmed since Ashraf Ghani succeeded Karzai in September last.
Of late, both Islamabad and Kabul have significantly toned down their rhetoric, and reports say Ghani has sought to reassure Pakistan that the new Afghan government is not working with India to undermine its interests.