Malaysia has accepted the Pope's statement of regret about his remarks linking Islam with violence after initially describing it as inadequate.
Prime Minister Abdullah Ahmad Badawi also urged the pontiff to avoid making hurtful remarks against Muslims.
The row began last week, when Pope Benedict XVI repeated criticism of the Prophet Muhammad by a medieval scholar.
The speech sparked worldwide protests by Muslims. The Pope said later the views he quoted were not his own.
The reversal in Malaysia's stance followed a meeting between Abdullah Ahmad Badawi and US President George W Bush at the sidelines of the UN General Assembly in New York.
The Malaysian prime minister, who is also chairman of the Organisation of Islamic Conference, said he discussed the Pope's comments during a 50-minute meeting with Mr Bush.
Earlier, the White House said Mr Bush had told the prime minister that the pontiff's regret was "sincere".
Protests against the Pope largely subsided in the Middle East on Tuesday but anger remained and there were calls for renewed demonstrations on Friday, the Muslim day of prayer.
In Egypt, the secretary general of President Hosni Mubarak's ruling National Democratic Party, Safwat el-Sherif, condemned the Pope's comments as a "misguided vision of Islam".
In Libya, the son of leader Moamer Kadhafi called on the pontiff to convert to Islam and dismissed his expression of regret. There were also small demonstrations reported in the Iranian cities of Qom and Teheran on Tuesday.
Iranian President Mahmoud Ahmadinejad late on Monday struck a more conciliatory tone than that of Supreme Leader Ayatollah Ali Khamenei, who accused the Pope of involvement in a "conspiracy to set in train a crusade".
Speaking in Caracas, President Ahmadinejad expressed respect for the Pope and noted the pontiff had "modified" his remarks.
The Pope on Sunday expressed regret for causing offence in last week's speech - delivered during a visit to his native Germany.
He said the medieval text he quoted, which said the Prophet Muhammad had brought the world only evil, did not in any way express his personal opinion.
"I hope this serves to appease hearts and to clarify the true meaning of my address, which in its totality was and is an invitation to frank and sincere dialogue, with mutual respect," he said.