However, the outgoing US president was unapologetic about the wars in Iraq and Afghanistan, saying that his country was "protecting" Muslims.
"Through the generations, our nation has helped defend the religious liberty of others - from liberating the concentration camps of Europe, to protecting Muslims in places like Kosovo, Afghanistan and Iraq," Bush said.
The UN has described the two-day conference in New York, which is sponsored by Saudi Arabia, as being designed to bridge differences between religions and cultures.
All 192 UN member states were invited to the event, which the king set up following one he helped organise in July in Madrid, Spain.
|Saudi police can detain those suspected
of changing their religion [EPA]
However, Saudi Arabia's involvment has sparked criticism from some rights
groups of its own record.
Sarah Leah Whitson, the Middle East director for Human Rights Watch, said a UN discussion on religious discrimination should spotlight places "where religious intolerance runs deepest, and that includes Saudi Arabia".
On Wednesday, the first day of the conference, Shimon Peres, the president of Israel, praised King Abdullah of Saudi Arabia for his Middle East peace initiative.
"I wish that your voice would become the prevailing voice of the region, of all people. It is right, it is needed, it is promising," he said.
Earlier, King Abdullah had said it was "high time" the world learned from history that differences between followers of different religions and cultures "engendered intolerance, causing devastating wars and considerable bloodshed without any sound logical or ideological justification".
The Saudi monarch called for all peoples and nations to promote peace, harmony and tolerance, saying "terrorism and criminality are the enemies of every religion and every civilisation".
Representatives of other Muslim states repeatedly stressed what they described as Western intolerance of Islam.
Asif Zardari, the Pakistani president, took up the theme on Thursday, saying that "imaginary fear of Islam has been rising".