The original German text of the Pope's lecture as published at the Vatican website differs slightly in several respects from the English translation, despite both versions being official (though "provisional") Vatican versions. It is unknown whether this had an impact on perceptions of the speech.

As for the emperor's quote employed by the Pope, the translation "evil and inhuman" is doubtful. What the Pope said in German, according to the audio recording of his address and the subsequent German text, was "nur Schlechtes und Inhumanes finden". The German adjective schlecht means "bad"; the English word evil would usually correspond to böse. The German adjective inhuman normally translates as inhumane which in English is subtly different from inhuman. As for meaning, therefore, "find only things which are bad and inhumane" seems to be a more accurate English translation of the Pope's utterance. (As a grammatical advisory, the use of initial capital letters indicates the two words are nouns. In this case they are adjectives being used as nouns, hence the introduction of the word "things" into the English translation.)

Another difference between the German original and the Vatican's English translation is the place where the word "jihad" has been omitted from the English: the original statement "The emperor touches on the theme of jihad, holy war" (kommt der Kaiser auf das Thema des Djihad, des heiligen Krieges zu sprechen) became in the English rendition "The emperor touches on the theme of the [sic] holy war." (In this context, the use of the word "the" before "holy war" is a grammatical mistake.)

The Rabbi went on to denounce Islamic violence against Christians, stating that "Our Muslim brothers would add respect to their religion if they outdid themselves and overcame the feelings of humiliation."

On 16 September 2006, Tarcisio Bertone, the Secretary of State of the Holy See, released a declaration explaining that the "position of the Pope concerning Islam is unequivocally that expressed by the conciliar document Nostra Aetate" and that "the Pope's option in favour of inter-religious and inter-cultural dialogue is equally unequivocal."

For many Muslim leaders, the declaration on 16 September was insufficient to rectify the situation. A representative for the Muslim Brotherhood rejected the Vatican statement, noting "Has he presented a personal apology for statements by which he clearly is convinced? No." Grand Mufti Abdul-Azeez ibn Abdullaah Aal ash-Shaikh, Saudi Arabia's highest religious authority, called the pope's declaration "lies", adding that they "show that reconciliation between religions is impossible." On the other hand, the Muslim Council of Britain had a more favourable view of the declaration, issuing their own statement on 16 September that the Pope's expression of "sincere regret" was "a good first step."

On 17 September, before his regular weekly Sunday Angelus prayer, Pope Benedict XVI stated the following:

The Angelus speech initially received a mixed yet predominantly negative response. Mohammed Sayed Tantawi, Grand Imam of Al-Azhar Mosque, Cairo, a Sunni institution, stated "We have no objection if the Pope holds another speech and declares publicly that what the Byzantine emperor had said was wrong. At the same time, the Pope has to apologize frankly and justify what he said," Mohammed Habib, deputy leader of the Muslim Brotherhood, Egypt's main Islamic opposition group originally, not long after the Pope's Sunday statements, called them a sufficient apology. However, later in the day, he retracted that statement, saying, "The Pope's comments that downplayed his earlier remarks are not enough. We will not accept anything less than an apology," Mohammed Habib also said: "It does not rise to the level of a clear apology and, based on this, we're calling on the Pope of the Vatican to issue a clear apology that will decisively end any confusion.

This sentiment was shared by the governments of Malaysia ("inadequate to calm the anger"), and Jordan ("a step forward", but "not sufficient"), by Turkish State Minister Mehmet Aydın ("you either have to say this 'I'm sorry' in a proper way or not say it at all. Are you sorry for saying such a thing or because of its consequences?") and scholar Yusuf al-Qaradawi, who called for a "peaceful international day of rage" on his popular TV show on Al Jazeera: "[The Pope's latest statements] were no apology. They were an accusation against Muslims that they didn't understand his words."