Sharif made the remarks during a meeting with visiting German Foreign Minister Guido Westerwelle.
The two leaders discussed bilateral relations and the regional situation.
"Drone attacks are violating our sovereignty as well as international laws. Drone attacks must stop. We have protested many a time. This is simply unacceptable," Sharif was quoted as saying in a statement issued by his office.
Pakistan is "ready to facilitate the withdrawal of coalition troops from Afghanistan and hopes that the Afghan army and security forces would be able to manage the situation" after the drawdown of US and allied forces next year, Sharif said.
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The protest was lodged on the instructions of the Prime Minister, the Foreign Office said.
Former envoy Tariq Fatemi, a Special Assistant to the Prime Minister, handed over a demarche to the US diplomat.
The drone strikes have emerged as a key irritant in Pakistan-US ties.
American officials have defended the use of drones, saying they are vital for targeting Taliban and al-Qaeda elements sheltering in Pakistan's tribal belt.
On May 29, the deputy chief of the banned Tehrik-e-Taliban Pakistan, Waliur Rehman, was killed in another drone strike in North Waziristan.
He said the attacks should stop as they were a violation of Pakistan's sovereignty.