The Southern Baptist Convention wants President Obama to cancel his appearance Sunday night at the 9/11 ceremony at Washington's National Cathedral.
The interfaith service, "A Concert for Hope," will include a Hindu priest, a Buddhist nun, and a Muslim imam.
However, it does not include a representative for evangelical Christians.
At least five faith leaders are scheduled to offer prayers at the service, but none of the individuals have been identified by the Cathedral.
"There is a tragic intolerance toward Protestants and particularly toward evangelicals, and I wish the president would refuse to speak unless it was more representative," Frank Page, president of the Baptist Convention's executive committee, told Fox News.
"The goal was to have interfaith representation," Richard Weinberg, the Cathedral's director of communications, told Fox News Radio.
"The Cathedral itself is an Episcopal church and it stands to reason that our own clergy serve as Christian representatives," he said.
Weinberg said the Washington National Cathedral serves as the "spiritual home for the nation" and as such "diversity was first and foremost" a factor in the planning.
Tony Perkins, president of the Family Research Council, told the radio network that the lineup for the memorial service was better suited for the United Nations than the United States.
"Three quarters of the American people identify as Christian and nearly a third of them are evangelical Christian," Perkins said. "And yet, there is not a single evangelical on the program."
The White House has referred all questions to the National Cathedral.