The pope's lecture last month at a German university led to violent protests around the world and at least two murders including the killing of an Italian nun in Somalia and a priest in Turkey.
In the open letter delivered on Sunday to the papal nuncio, the Vatican's envoy in Jordan, the signatories said: "We must point out some errors in the way you [the pope] mentioned Islam as a counterpoint to the proper use of reason, as well as some mistakes in the assertions you put forward in support of your arguments."
In particular the scholars focused on perceptions of forced conversion, jihad versus holy war and the relationship between Christianity and Islam.
But those who signed the letter, including the Grand Muftis of Egypt, Russia, Kosovo, Oman and Istanbul, also said they appreciated the pope's personal expression of sorrow over his citing of anti-Islamic quotes by a 14th-century Byzantine emperor.
Islamica magazine, which published the letter on its website, said since signatories of all eight schools of thought and jurisprudence in Islam, including a woman scholar, are represented in the letter it "is unique in the history of interfaith relations".
Mohammed Samiullah Khan, managing editor of the magazine, told Aljazeera: "It was unprecedented that all these scholars came together.
"It took time, of course, to work out the text and get the right response. It obviously couldn't happen overnight. But we think it addresses the pope's speech in a very constructive way.
"The initiative was taken by the scholars themselves, there was a large group of scholars who felt a correct response needed to be made and collectively they formulated the letter. It must be emphasised that this was a collaborative effort."
"Holy war" dispute
The letter points out that "holy war", referred to in the speech, is a term that does not exist in Islamic languages.
It says it should be emphasised that jihad means struggle, and specifically struggle in the ways of God. This struggle may take many forms, and although this includes the use of force, it does not necessarily mean war.
With regard to perceptions of "forced conversion", the scholars say that the argument that Muslims are commanded to spread their faith "by the sword", or that Islam was largely spread "by the sword", does not hold up to scrutiny.
It points out that while as a political entity Islam was spread partly as a result of conquest, the greater part of its expansion came as a result of preaching and missionary activity. Moreover, Islamic teaching did not prescribe that conquered populations be forced or coerced into converting.
In his speech, the pope cited the emperor's assertion that "anything new" brought by the Prophet was "evil and inhuman", such as the alleged command to spread by the sword the faith he preached.
The scholars state that what the emperor failed to realise, aside from the argument above that no such command existed anyway in Islam, "is that the Prophet never claimed to be bringing anything fundamentally new and that according to Islamic belief, all the true prophets, preached the same truth to different peoples at different times".
The laws may be different, says the letter, but the truth is unchanging.
Appeal for dialogue
The signatories said that they appreciated the pope's assurance that the words of the emperor cited did not reflect his personal opinion.
They said that by following the Quranic precept of debating "in the fairest way" they hoped to reach out so as to increase mutual understanding, reestablish trust, calm the situation for the sake of peace and preserve Muslim dignity.
Following the handing in of the letter, Khan said: "The aim of this letter was to address the pope's speech in an appropriate manner.
"We haven't had any response from the Vatican yet ... they have to make their own deliberations and then respond to the letter in due course, the important thing is that a constructive dialogue has been started."