The Dove World Outreach Centre, in Gainesville, Florida, plans to mark Saturday's ninth anniversary of the 11 September attacks by burning copies of Islam's holy book, in what it says will be a warning to radical Muslims.
The UN and an umbrella body representing aid groups in Afghanistan warned Wednesday that civilians and aid workers in the country could be killed if the church goes ahead with the plan.
Earlier, the US commander of foreign forces in Afghanistan, General David Petraeus, said the evangelists would be putting US troops in danger if they went ahead with their demonstration.
The Vatican's Pontifical Council for Interreligious Dialogue in a statement it had "received with great concern the news of the proposed "Koran Burning Day" and called the event "an outrageous and grave gesture".
"Each religion, with its respective sacred books, places of worship and symbols, has the right to respect and protection," the council said.
A senior Muslim Brotherhood official, Essam al-Erian, said in Cairo that the outdoor Florida ceremony would be a "barbaric act reminiscent of the Inquisition" and would "increase hatred towards the United States in the Muslim world".
European Union foreign affairs chief Catherine Ashton also publicly condemned the plans.
There have already been protests in the Afghan capital Kabul and in Indonesia against Jones's plans, while Iran has warned it could unleash an uncontrolled Muslim response.
Saturday's anniversary is set to coincide with festivities for Eid al-Fitr, which marks the end of the holy month of Ramadan, a time of prayer and fasting for nearly 1.5 billion Muslims worldwide.
For the moment, Dove World Outreach Centre pastor, Terry Jones, remained defiant.
"Instead of us being blamed for what other people will do or might do, why don't we send a warning to them?" he said.