“I expressly condemn the attack on the German embassy in Khartoum and demand from the Sudanese authorities and government that the integrity and security of the embassy is restored,” Foreign Minister Guido Westerwelle said in a press conference on Friday afternoon.
“I understand the fury in the Islamic world at the anti-Islamic hate video and I condemn this video, but this is no justification for violence and the storming of embassies or endangering of people's lives. The video is unacceptable and hurts the feelings of millions of believers but this is no justification for violence,” he said.
Westerwelle also confirmed that the embassy staff were safe despite the storming and torching of the embassy building.
In an attempt to reach a global audience, Westerwelle repeated the part of his statement concerning his condemnation of the video in English.
Around 5,000 people surrounded the German and British embassies, which are next door to each other in Khartoum, after Friday prayers initial reports said.
Sudanese police fired tear gas to disperse the protesters as several of them scaled the roof of the German embassy and tore down the German flag, replacing it with a black Islamic one.
The mob then proceeded to smash windows, broke into the building and started fires.
Afterwards hundreds gathered in front of the US embassy, and were beaten back by security forces. Broadcaster Al-Arabija reported that one demonstrator was killed as tear gas was fired into the crowed. A cameraman from the station was injured.
Westerwelle said the Sudanese ambassador in Berlin had been summoned to the foreign ministry on Friday morning where he was reminded of his government's duty to protect diplomatic institutions.
Germany's ambassador to Sudan, Rolf Welberts, only took up his position last Saturday. He has been in contact with Westerwelle, informing him of the situation.
Friday's attack was the latest in a series initially directed at US embassies in several Muslim countries, as anger sparked by a film mocking Islam spread across the Muslim world.
Westerwelle said on Friday morning that security measures had been bolstered at embassies in Muslim countries, and that German soldiers stationed in Afghanistan had also been put on a higher state of alert.
The US ambassador to Libya was killed and three others injured when the consulate was attacked in the city of Benghazi on Tuesday.
A further four people were killed at the US embassy in Yemen on Thursday after similar attacks, while some 220 people were injured in anti-US protests in Cairo.
The protests began after the video - an amateurish film denigrating the Prophet Mohammed allegedly linked to evangelical and Coptic Christians in the United States - was released.
Demonstrations have spread across the Middle East, as well as to Bangladesh, Iran, Iraq, Israel and the Gaza Strip, Kuwait, Sudan and Tunisia.