The militants ambushed the convoy as it travelled through the volatile southeastern Paktia province ahead of a planned by President Hamid Karzai to Urgun district, where a devastating suicide attack killed 41 on Tuesday.
The attack underlines the fragile security situation Afghanistan faces as NATO progressively withdraws its 50,000 remaining combat troops, leaving local forces to battle a resilient Taliban insurgency.
"The security team was travelling to Urgun district (in neighbouring Paktika province to prepare for the president's visit there," top presidential spokesman Aimal Faizi told AFP.
The convoy pushed ahead despite the attack, Faizi added, facing two more ambushes by insurgents on the way, but reached its destination without sustaining any further casualties.
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A security source in the region said four vehicles of the president's security convoy were also damaged by rocket fire.
The main highway connecting Kabul to Afghanistan's southern regions is often the sight of insurgent ambushes.
The attack in Urgun took place in a bustling market place and was one of the deadliest in the war-torn country for months.