"The government of Pakistan strongly condemns the killing of US Ambassador Christopher Stevens and several other staff members in an attack on the US Consulate in Benghazi, Libya," Foreign Office spokesman Moazzam Khan said in a statement tonight.
Stevens, 52, and three other American officials died as gunmen protesting over the film fired rocket-propelled grenades at the envoy's car and set fire to the US mission.
President Barack Obama too condemned the killing of the ambassador.
Pakistan also condemned the emergence of a clip from the anti-Muslim film.
"The government of Pakistan strongly condemns the airing of a defamatory video clip in the US, maligning the revered and pious personality of Prophet Mohammed on the eve of September 11, 2012," spokesman Khan said in a separate statement.
Khan said the emergence of the video at a time when the world was marking the anniversary of the 9/11 terror attacks had created "enmity" between people of different faiths.
"Such abominable actions, synchronised with commemoration of atrocious events like 9/11, provoke hatred, discord and enmity within societies and between peoples of various faiths. The event has deeply hurt the feelings of the people of Pakistan and the Muslims all over the world," he said.
Pakistan is a "strong proponent of inter-faith harmony and believes that all manifestations of extremist tendencies must be opposed", Khan said.
In neighbouring Afghanistan, Taliban leaders called on people to "take revenge" on American soldiers for the US-made film.
A clip from the film promoted on YouTube by extreme anti-Muslim groups in the US triggered protests in Libya, Egypt and Tunisia.
Protests in the Muslim world on such issues have usually triggered similar demonstrations by extremist groups in Pakistan.
Throughout the day, reports suggested that the Pakistan government could take action against YouTube for hosting the clip from the film, made by an Israeli-American.
Muslims consider it offensive to depict Muhammad in any manner, including in paintings and movies.
The 2005 publication of caricatures of the Prophet Muhammad in a Danish newspaper triggered riots in many Muslim countries, including Pakistan.
Islamabad: Pakistan on Wednesday condemned the killing of the US Ambassador in Libya during protests against an anti-Islam film but said that the movie had "deeply hurt" the feelings of Pakistanis and Muslims around the world.
First Published: Wednesday, September 12, 2012, 23:43