The mayor's office says the annual ceremony at ground zero focuses on families and has never included clergy invocations.
However, critics say the mayor is discriminating against religious people. Among the protesters are the Catholic League, the Family Research Council and the Southern Baptist Convention.
The event includes moments of silence and readings. President Barack Obama and other political leaders will attend.
Few city religious leaders have complained. Roman Catholic Archbishop Timothy Dolan says he talked to the mayor about the ceremony and the archbishop accepts that the program has to be limited. The New York Board of Rabbis says Bloomberg works closely with religious leaders.