Speaking at the opening of the conference in Berlin, Friedrich said, "We won't allow the Salafists to set our agenda with their propaganda," but he added that an "important signal" needed to be sent.
The Salafists, one of the strictest branches of Islam, caused a media controversy last weekend by handing out free copies of the Koran in several German cities.
This year's Islam conference is to concentrate on the position of Muslim women in German society, but a number of politicians, including Lower Saxony state Interior Minister Uwe Schünemann, had called for a "clear signal" to address the Salafist Koran giveaway.
Friedrich also said that the conference's declaration against domestic violence and forced marriage was the first time that Muslims of various backgrounds had "agreed on a text that unambiguously condemned such practices."
Theologian Tuba Isik-Yigit told the Süddeutsche Zeitung that she would like the conference to address the fears of many immigrants following the revelation of a series of far-right murders last year.
The conference was first called by former Interior Minister Wolfgang Schäuble in 2006 as a forum for discussion between Germany's Muslims and the state.
Friedrich praised the progress that had been made since then, particularly the introduction of Islam into religious education in schools.
Volker Kauder, chairmen of the Christian Democratic Union's parliamentary faction, garnered criticism ahead of the conference by saying, "Islam is not part of our tradition and identity in Germany and so does not belong to Germany."
He then added, "Muslims do belong to Germany. Of course they enjoy the same rights as citizens."
Green Party chairman Cem Özdemir dismissed Kauder's distinction as "absurd," and accused him of pandering to the conservative end of his party. "Presumably, Kauder also thinks that the women's movement does not belong to Germany, but women do."
Kenan Kolat, head of Germany's main Turkish community organization, was more abrasive about Kauder's remarks. "Everyone can talk rubbish in this country. That's possible in a democracy."