The raids were carried out at the same time as German Interior Minister Thomas de Maiziere imposed a ban on the group, which was set up in Cologne in 2005 by a Palestinian immigrant called Ibrahim Abou-Nagie.
Since 2011 Abou-Nagie and his fellow missionaries have carried out the controversial "Read" campaign, which distributes free copies of the Koran to passers-by at transport hubs or shopping centers.
Abou-Nagie has also sought to spread his campaign to Austria, France, Sweden and Brazil. The Salafist preacher was in Malaysia at the time of the raid.
"This was a surprise for me too, I don't know about these people or this group's activities. However, my first comment would be this: following the Koran doesn't mean practicing something which can be detrimental to others," El-Zoghbi said.
"Here it is appropriate to quote Pope Francis, who held up the Koran and said, 'This is a book of peace, not war!"
El-Zoghbi also expressed disagreement with some of the terminology used to describe Islamic groups. For example, the use of the word "Salafist" in connection with what he terms a political organization.
"Salafism" describes a fundamentalist form of Sunni Islam which condemns theological innovation, advocating strict adherence to sharia law and the institution of a theocratic Islamic state.
The German government has described the Salafi movement as "a particularly radical form of Islamism," with close links to terrorism.
On Wednesday German CDU politician Wolfgang Bosbach told Sputnik Deutschland that the movement is "unacceptable for a state of law," because its followers "put the words and deeds of the prophet and his revelation above secular law."
"The word 'Salafist' means 'ancestor.' These are people who act according to tradition and old regulations. This is an example of how words today are being hijacked and used in the wrong way; it's actually painful to hear."
"For example, the word 'jihad' to us signifies a sense of spiritual elevation, but it has been presented as a religiously-motivated war. These are misrepresentations, and we have an obligation to repudiate them."
El-Zoghbi was clear that the Fambras association of Muslims has no connection with The True Religion, and rejects the movement.
"These people are criminals and anybody who is aware of their activities should inform the police of their activities. We, Fambras, have no connection with criminal or terrorist activity, especially when these killers who link themselves to the Islamic faith. We don't consider them as such (Muslims), because we are peaceful," El-Zoghbi said.
