A statement issued by Foreign Office spokesman Moazzam Khan said Pakistan "strongly condemns the attack in Kabul yesterday that wounded Mr Assadullah Khalid, head of the Afghan National Directorate of Security".
"Our thoughts and prayers are with him. We hope for his early recovery," the statement said.
Khan said Pakistan "remains committed to peace and stability in Afghanistan".
He added: "The two countries face the common threat of terrorism. We will continue to work closely with Afghanistan to eliminate this scourge".
Khalid was in a stable condition in a US-run military hospital near Kabul after the Taliban assassination attempt, officials in the Afghan capital said today.
He was targeted by a suicide bomber posing as a Taliban peace envoy in a spy agency guesthouse.
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Last year, Afghan High Peace Council chief Burhanuddin Rabbani was assassinated by a bomber posing as a Taliban peace envoy with explosives hidden in his turban.
Afghan officials had then alleged that the bomber had come from Pakistan, a charge that was denied by Islamabad.