Salman Shaikh, director of The Brookings Doha Center in Qatar, said Monday the Islamists' declaration will unsettle both Western backers of the Syrian opposition and groups inside Syria, ranging from secularists to the Christian minority.
"They have to feel that the future of their country could be slipping away," Shaikh said. "This is a sign of things to come the longer this goes on. The Islamist groups and extremists will increasingly be forging alliances and taking matters into their own hands." The West is particularly concerned about sending weapons to rebels for fear they could end up in extremists' hands.
In Washington, State Department spokeswoman Victoria Nuland said that since the new opposition group has endorsed pluralism and tolerance, "it's not surprising to us that those who want an extremist state, or a heavily Islamist state in Syria have taken issue with this."
The Islamists' announcement, made in an online video released Sunday, shows the competing influences within the rebellion, between religious hard-liners who want to create an Islamic state in Syria including foreign al-Qaida-style jihadi fighters and the newly formed Syrian National Coalition, which was created earlier this month in hopes of uniting the disparate groups fighting Assad's regime.
The National Coalition was formed under pressure from the United States, which sought a more reliable partner that nations could support. Key to its credibility is whether it can ensure the support of the multiple, highly independent rebel brigades battling on the ground across the country within Syria, which largely ignored the previous opposition political leadership, made up of exiles.
In the new video, 13 Islamic radical factions denounced the coalition as a foreign creation.
Most important among them were the al-Tawheed Brigade, which is one of the largest rebel groups operating in Aleppo, and Jabhat al-Nusra Arabic for "the Support Front" which is mainly made up of foreign jihadi fighters. Jabhat al-Nusra has become notorious for suicide bombings targeting regime and military facilities and is at the forefront of fighting in Aleppo.
"We are the representatives of the fighting formations in Aleppo and we declare our rejection of the conspiratorial project, the so-called national alliance," an unidentified speaker said in the video. "We have unanimously agreed to urgently establish an Islamic state."
He spoke at the head of a conference table where about 20 others were gathered, with a black Islamist flag behind them.
The authenticity of the video could not be independently confirmed, but it was released on a website that carries al-Qaida and other militant statements, as well as on the al-Tawheed Brigade website.
The new opposition bloc, formed Nov. 11 in Qatar, is trying to allay fears of extremism within the rebellion. A moderate cleric, Mouaz al-Khatib, was chosen as its leader in an attempt to establish the movement's religious credentials with the public while countering more radical factions.
In Cairo, al-Khatib played down the significance of those who reject the alliance, saying, "we will keep in contact with them for more cooperation in the interest of the Syrian people." He also announced that the coalition would be headquartered in the Egyptian capital.
The coalition is gaining some traction internationally. France was the first Western nation to recognize it as the only legitimate representative of the Syrian people. France also welcomed a member of the Syrian opposition as the country's ambassador.
Turkey and the six-nation Gulf Cooperation Council also recognized the group as the representative of the Syrian people.
But the United States and Italy have been somewhat less forthcoming. President Barack Obama has said the U.S. needed more time and wanted to make sure that the group "is committed to a democratic Syria, an inclusive Syria, a moderate Syria."
He also says the U.S. isn't considering sending weapons to the opposition because of concerns the arms might fall into the hands of extremists.
Italy took a similar view, recognizing the opposition as legitimate but stopping there.
On Monday, European Union foreign ministers gave the bloc a vote of confidence but stopped short of offering official diplomatic recognition because that can only be decided by each member country individually. Still, the endorsement of the coalition as a legitimate voice for Syria's people represents a major step forward in Western acceptance for the group.
"The EU considers them legitimate representatives of the aspirations of the Syrian people," the bloc's 27 foreign ministers said in a statement at the end of their monthly meeting in Brussels.
Some EU members have suggested arming the Syrian opposition, but the idea has gotten little traction.
Currently, the EU has an embargo prohibiting the shipment of arms into Syria, which is likely to be renewed later this week. A senior EU official said last week that shipping weapons to Syrian rebels while keeping an embargo against the Assad regime in place would be difficult to enforce.
The violence in Syria threatens to inflame an already combustible region. The fighting already has already spilled into Israel, Lebanon, Jordan and Turkey.
Germany's defense minister said Monday he expects Turkey to make a formal request to NATO for Patriot missiles to bolster anti-aircraft defenses along the border with Syria.
"It may be I expect it that there will be a request by the Turkish government to NATO today for Patriot missiles to be stationed on the Turkish border," Thomas de Maiziere said ahead of the EU meeting.
NATO's Secretary-General Anders Fogh Rasmussen said no such request had been received yet from Ankara, but that if it was it would be considered "as a matter of urgency."
"The situation along the Syrian-Turkish border is of great concern," Fogh Rasmussen said as he arrived for a meeting with the European Union's foreign and defense ministers. "We have all plans in place to defend and protect Turkey if needed."
Although the civil war has left Assad isolated internationally, Iran has stuck by Damascus.
Iran's semi-official Fars news agency said Monday that Tehran has started building a $10 billion natural gas pipeline to Syria as part of efforts to boost Iran's energy sector, which has been battered by international sanctions.
The 1,500-kilometer (900-mile) pipeline will pass through Iraq before reaching Syria.
Associated Press writers Barbara Surk in Beirut, Suzan Fraser in Ankara, Turkey, Maamoun Youssef in Cairo, Matthew Lee in Washington and Slobodan Lekic and Don Melvin in Brussels contributed to this report.