"The government of Afghanistan strongly rejects reports alleging that the Peshawar attack was planned and controlled from Afghanistan," Khaama press late Saturday quoted Ghani as saying.
The Afghan government, in a statement, dismissed the reports terming it baseless and reiterated Kabul's stance that the country would never be allowed to be used against other nations.
"Afghanistan feels the pain and agony inflicted by terrorism and offers condolence to the victims of the terrorist attack," the statement said, adding terrorism is the enemy of the humanity and never recognises good or bad.
The governments of Afghanistan and Pakistan must work jointly to eliminate terrorism from the region and Islamabad must fight all terrorist groups without distinction, the statement added.
Pakistani military officials had claimed that Friday's attack on Pakistan Air Force base in Peshawar was planned from Afghanistan. The attack claimed 42 lives.
A group of 13 Pakistani Taliban guerrillas stormed the air force base and killed at least 29 people of the Pakistan Air Force and army, including an army captain.