Megawati, in a speech opening the conference on Monday, described the war in Iraq as "exceptional injustice" against a Muslim country.
"It may be due to coincidence or intention, but an exceptional injustice is apparent in the attitude and actions of big countries toward countries whose majority of populations are Muslims," said the president of the world's largest Muslim-populated nation.
"The act of violence undertaken unilaterally against the Republic of Iraq by certain countries, which are now finding it difficult to prove the existence of weapons of mass destruction there, which is the sole justification to launch the biggest military attack at the beginning of the 21st century, is an evident picture of this injustice," she said.
The three-day conference is attended by some 300 delegates from 49 countries, including Western students of Islam.
It is aimed at promoting dialogue between the Islamic world and the West in view of tensions resulting from the US-led global war on terror, perceived by many in Muslim countries as targeting Islam.
The meeting is organised by Indonesia's largest Islamic organisation, the Nahdlatul Ulama (NU), in cooperation with the government.
Megawati's view was echoed by NU chairman Hasyim Muzadi, who criticised the US-led campaigns in Iraq and Afghanistan.
"We need to search for similarities among the religious traditions that are so rich, which we must believe originate from the same god, and turn them into the basis to build a better world"
"An attack against a country under any pretext will only bring untold misery to innocent civilians," Muzadi told delegates.
"The attackers also stand to lose, at least as far as global opinion is concerned, not to mention if it is launched without the authorisation of the United Nations," he said.
NU claims a following of 40 million Indonesians.
Headscarf ban criticised
Megawati also criticised the French government's decision to ban conspicuous religious symbols including Islamic headscarves at government schools, calling the move "injustice in a far smaller feature".
"Whether they realise it or not, those discriminative acts constitute as test cases whether those big countries are serious in practising the human rights that they have preached to the whole world since the 20th century," she said.
Megawati urged Islamic scholars to prove wrong a thesis that the world would in future be characterised by religious conflicts.
"We apparently need to search for similarities among the religious traditions of humankind that are so rich, which we must believe originate from the same god, and turn them into the basis to building a better world," she said.