The official protest was lodged amid widespread protests in Pakistan against the anti-Islam movie, which has also prompted violent protest in parts of the Muslim world.
Angry protesters Friday burnt two cinema houses in the northwestern city of Peshawar, where a TV cameraman was also killed during clashes between the police and the demonstrators.
The Pakistani government called for peaceful protest and declared Friday as a national holiday to facilitate the people to join the protest.
Prime Minister Raja Pervez Ashraf spoke at a largely-attended gathering in Islamabad and condemned the anti-Islam movie and stressed that no one should insult religions under the excuse of the freedom of expression.
The foreign ministry said the American diplomat was further conveyed that the US government should immediately take measures to remove the sacrilegious video from YouTube and take action against its author, a statement said.
Ambassador Hoagland was reminded that all faiths need to promote inter-religious harmony and tolerance.
"The intentional spread of hatred among faiths is an attack on humanity itself," the foreign ministry said.
The statement said Hoagland reiterated his government's position as well as that of the US leadership that they strongly condemned the video.
"The video was disgusting and was an act of one aberrant individual," the foreign ministry statement quoted the American diplomat as saying.