President Obama and Indonesian President Susilo Bambang Yudhoyono attend the official arrival ceremony at State Palace Complex-Istana Merdeka in Jakarta, Indonesia, on Tuesday. (Associated Press)

An Indonesian Muslim woman holds posters during a protest against the visit of President Obama in front of the U.S. Embassy in Jakarta, Indonesia, on Tuesday. In an address at the Univeristy of Indonesia, Mr. Obama said that international problems only can be solved through partnership. (Associated Press)

By Kara Rowland

-Building on his previous efforts to reach out to the Muslim world, President Obama stressed Wednesday that the United States “is not and will never be at war with Islam,” and extolled before a crowd of Indonesian students the possible benefits of collaboration on entrepreneurship, technology and education.

The address, which Mr. Obama delivered at the University of Indonesia in Jakarta, represented a follow-up to his watershed speech in Cairo last year, when he called for a new beginning in relations between the United States and Islamic nations. This time around, the president — who spent four years in Indonesia as a boy — acknowledged that “no single speech can eradicate years of mistrust,” telling an audience in the world’s largest Muslim-majority country that international problems only can be solved through partnership.

“We do have a choice: We can choose to be defined by our differences, and give in to a future of suspicion and mistrust. Or we can choose to do the hard work of forging common ground, and commit ourselves to the steady pursuit of progress,” said Mr. Obama, according to prepared remarks released by the White House. “In the 17 months that have passed [since the Cairo speech] we have made some progress, but much more work remains to be done.”

Mr. Obama gave the address before heading to Seoul later in the day for the Group of 20 summit. He spent three days in India before arriving in Jakarta, where he lived with his mother and his Indonesian stepfather from 1967 to 1971.

The remarks come on the heels of Mr. Obama’s strong public criticism of Israel’s announcement that it plans to build new settlements in East Jerusalem. After a meeting with Indonesian President Susilo Bambang Yudhoyono on Tuesday, the president said he was “concerned” by the news, which “is never helpful when it comes to peace negotiations.”

The ongoing dispute between the Israelis and Palestinians also was a focus of Mr. Obama’s address to students. While he touted the fact that both sides have agreed to restart direct talks, he cautioned that “enormous obstacles remain” to achieving a two-state solution.

Mr. Obama also focused on the threat posed by al Qaeda, citing Indonesia’s own experiences with Islamic extremists and drawing a clear distinction between the terrorist organization and everyday Muslims.

“All of us must defeat al Qaeda and its affiliates, who have no claim to be leaders of any religion — certainly not a great, world religion like Islam,” said Mr. Obama, according to the remarks. “But those who want to build must not cede ground to terrorists who seek to destroy. This is not a task for America alone. Indeed, here in Indonesia, you have made progress in rooting out terrorists and combating violent extremism.”

In the months since Mr. Obama’s 2009 visit to Cairo, several events underscored the persistence of the terrorist threat, including botched attempts to bomb a flight to Detroit on Christmas and an SUV in Times Square earlier this year. More recently, anti-terrorism officials in Britain and Dubai discovered explosive packages from Yemen in cargo planes en route for the U.S.

Meanwhile, Mr. Obama has moved to wind down the war in Iraq while escalating operations in Afghanistan. He ordered a surge of some 30,000 additional troops there in December.

But while he touched on the security-related issues, Mr. Obama clearly sought to emphasize other bonds with Indonesia, reflecting on his memories as a child and praising the Asian nation’s “democratic transformation” since then. His administration announced a swath of new partnerships with the country, including a new entrepreneurship program that will be funded in part by the State Department and a five-year, $88 million initiative aimed at improving the quality of higher education in Indonesia.

Mr. Obama has been joined on his Asian trip by first lady Michelle Obama, who was the focus of a small controversy in Indonesia on Tuesday after a conservative Muslim government minister said he tried to avoid a handshake with her for religious reasons but was unable to do so. The comments by the minister, who stood in a receiving line to meet the Obamas upon their arrival, set off a debate on the Web over the incident after video footage appeared to show the official enthusiastically reaching for her hand.

Some Indonesians reportedly were disappointed by the brevity of Mr. Obama’s trip, which had to be cut even shorter due to an expected ash cloud from Mount Merapi, an erupting volcano. The trip was previously canceled twice this year due to domestic concerns over the health care bill and the BP oil disaster.