The two-day event is being held in Doha the absence of some Muslim religious figures, who declined to attend due to invitations extended to Israeli Jewish rabbis.
Conference participants will mainly discuss areas of agreement among the three faiths, Aljazeera said.
Three Israeli rabbis who received invitations to the dialogue decided to stay away, however, after being denied their requests to make opening speeches.
Organiser Aisha al-Mannai said on Wednesday that the three Israeli rabbis who were invited "had made their excuses".
"They said they would only take part if they could make one of the opening speeches. Unfortunately we had already finalised the line-up, which of course includes one opening speech by a Jewish representative and there would have been other opportunities to contribute during the various sessions."
Al-Mannai said eight or nine rabbis from outside Israel were still due to attend the Doha conference, which is being jointly sponsored by the University of Qatar and the Qatari Foreign Ministry.
It is the third edition of the inter-faith dialogue in Qatar but the first to which Jewish representatives have been invited. More than 80 clerics are expected to attend.
The Israeli rabbis' decision had its "positive" side, al-Mannai added, as some of the clerics who had planned to stay away in protest against their presence, like Iran's Ayat Allah Ali Taskhiri, were now coming.
There was no immediate word on the plans of Egypt's Coptic patriarch Pope Shenuda III or Egyptian-born Muslim cleric Sheikh Yusuf al-Qaradawi, both whom had also announced boycotts.