"We have come here to put an end to terrorism and its bitter consequences," Moualem said. "Diplomacy and terrorism cannot go in parallel. Diplomacy must succeed by fighting terrorism."
Syria's government agreed to attend the talks but rejects the premise that the goal is to establish a temporary government to replace Assad. Russia, a sponsor of the conference, insists that Assad's ouster is not a foregone conclusion. On Wednesday, Russian Foreign Minister Sergei Lavrov urged delegates not to "predetermine the outcome."
Opposition leader Ahmad al-Jarba said the rebels will never accept a negotiated settlement that keeps Assad in power, and he suggested that further talks are pointless if the regime rejects the premise of a transitional government.
Jarba implored the delegates from more than 30 nations to move quickly to end the conflict.
"Time is like a sword," he said through an interpreter. "And for the Syrian people, time is now blood."
Other opposition figures and the Syrian government said the talks are on track. Jarba's coalition had resisted attending for months, fearing that the conference would only solidify Assad's military gains and further divide the mostly expatriate political opponents and the front-line rebels.
Lakhdar Brahimi, the special U.N. and Arab League envoy to Syria, told reporters that he may need more time to discuss the terms of Friday's scheduled talks before bringing the two sides into the same room.
Those direct negotiations, planned for nearby Geneva, would be the first extended talks between Syria's government and opposition forces and would take place only in the presence of mediators from the United Nations.
The gathering opened amid renewed allegations of widespread human rights abuses by Assad's government. A report by three former war crimes prosecutors accuses the regime of the systematic torture and execution of about 11,000 prisoners since the uprising began. Several speakers Wednesday referred to the new allegations, which appear to back up rebel claims of torture and may help draw support for the opposition cause.
Wednesday's round of speeches by the attending foreign ministers offered an opportunity for the world to show support for a diplomatic effort to end the conflict. Secretary of State John Kerry, like many other speakers, said the only solution to a war that has killed more than 130,000 people is a political settlement between Assad and his opponents.
But Kerry, who has called the Syrian president a killer unworthy of his office, reiterated the U.S. demand for a new government.
"We need to deal with reality here," Kerry said. "Bashar Assad will not be part of that transition government."
When it was his turn to speak, Moualem rebuked the chief U.S. diplomat directly.
"No one, Mr. Kerry, in the world has the right to give legitimacy or to withdraw legitimacy from a president, a government, a constitution or a law or anything in Syria, except Syrians," he said.
Moualem also argued with U.N. Secretary General Ban Ki-moon, the conference host, who interrupted Moualem when his speech ran past his allotted eight minutes.
"You live in New York. I live in Syria," Moualem retorted. "I have the right to give the Syrian version here in this forum. After three years of suffering, this is my right."
"Let me finish my speech," Moualem said angrily, and Ban let him go on.
Moualem told the delegates that al-Qaida-linked militants fighting Syrian troops have steadily gained ascendancy in the rebel-held north of the country. He disputed the characterization of the war as an uprising or internal "revolution," saying that the fighters battling Assad's troops come from more than 80 nations.
Many of the nations represented here have backed the rebels, sending arms, money or other help. While Russia, an ally and military supplier to the Assad regime, is participating in the talks, Iran - Syrian's staunchest military patron - was excluded.
In a mark of the high emotions on all sides, the closing news conference with Brahimi and Ban erupted in shouting, as Syrian journalists accused Ban of ignoring their questions.
Syrian activists who came to cover the meeting for opposition news organizations expressed disappointment that the government was so uncompromising.
"Nothing has changed," said Adnan Hadad of the Aleppo Media Center. "They came here to say the same old stuff they've been saying for the past three years."
Still, Wednesday's nine-hour session of speeches was notable because members of the Syrian opposition and the government sat in the same room without walking out. Ban said afterward that the discussions were cordial, and Kerry said the initial confrontations were to be expected.
"Opening positions are opening positions," he told reporters. He set no timetable for the negotiations but suggested that they will be lengthy and difficult. "Talk takes a while," Kerry said.
Diplomats and U.S. officials caution that political breakthroughs are unlikely now. Rather, they say, the effort begun Wednesday will focus on confidence-building measures such as local cease-fires and deliveries of humanitarian aid - steps that might help build wider support for a peace process ahead of future talks.
Diplomats attending the session said the two sides' uncompromising public posturing concealed a deeper desire to see at least some results emerge from the negotiations.
"This was their public position," said Iraqi Foreign Minister Hoshyar Zebari. "It was very obvious they were raising the rhetoric. I think their private positions will be different. . . . We don't know what will happen in closed rooms."
The day ended on a more conciliatory note. In final comments, a more subdued Moualem said the conference had "charted the first steps to dialogue."
Jarba added, "We have to open the way for negotiations."
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Suzan Haidamous, Susannah George and Ahmed Ramadan in Beirut contributed to this report.