The letter has signatures from 38 experts, including grand muftis from the Muslim world and scholars based in Britain and the US.
They said they accepted the pontiff's stated regrets over the uproar, but challenged his area of expertise, criticising his misreading of the Quran, his failure to use terms correctly and his use of obscure and possibly biased sources.
"The letter represents an attempt to engage with the papacy on theological grounds in order to tackle wide-ranging misconceptions about Islam in the Western world," said Islamica Magazine, an international quarterly on Muslim affairs that posted the open letter on its website on Saturday.
Mohammad Khan, the magazine's managing editor, said a copy of the letter would be handed to the Vatican nuncio (ambassador) on Sunday in Amman, where Islamica has an editorial office.
Protests across the Muslim world were sparked after Pope Benedict quoted a 14th century Byzantine emperor as saying Islam was evil and irrational and had been spread by the sword.
Benedict has said he did not agree with the emperor he quoted.
The scholars included grand muftis of Egypt, Oman, Uzbekistan, Istanbul, Russia, Bosnia, Croatia and Kosovo as well as a Shia ayatollah, Jordanian Prince Ghazi bin Mohammad bin Talal and Western-based academics.
"Had Muslims desired to convert all others by force, there would not be a single church or synagogue left anywhere in the Islamic world"
From the Muslim scholars' open letter to Pope Benedict
They faulted Benedict for arguing that a Quran verse advocating religious freedom was written while the Prophet Muhammad was politically weak and "instructions ... concerning holy war" written when he was strong.
The verse was written when Muhammad ruled in Medina and wanted to keep converts from forcing their children to abandon their Christian or Jewish faith for Islam, they wrote.
The letter also faulted him for translating "jihad" as "holy war", saying "jihad" means a "struggle in the way of God" and did not necessarily have to include force.
The scholars also disputed passages where he said or implied that Islam was irrational, violent and based on forced conversion.
"Had Muslims desired to convert all others by force, there would not be a single church or synagogue left anywhere in the Islamic world," they wrote.
They asked how Benedict could argue that violence was against God's nature when Jesus Christ used it to drive the money-changers out of the Temple in Jerusalem.
It would be better to say cruelty, brutality and aggression were against God's will, they argued, adding that the Islamic concept of jihad also condemned these scourges.
The letter acknowledged that some Muslims used violence "in favour of utopian dreams", but said this went against Islamic teaching. They specifically condemned the murder of an Italian nun in Somalia, which followed the pontiff's speech.
The scholars also criticised Pope Benedict for basing his view of Islam on books by two Catholic writers, saying Christians and Muslims should "consider the actual voices of those we are dialoguing with, and not merely those of our own persuasion".