Several Iranian officials and media also condemned the conference Tuesday and urged Arab countries not to compromise with the Israelis.
Hossein Shariatmadari, an adviser to Ayatollah Ali Khamenei, told Asharq Al-Awsat newspaper that Iran, an ally of Damascus, was surprised by Syria's decision to take part in the Annapolis, Maryland meeting aimed at trying to broker a peace deal between Israel and the Palestinians.
"We were surprised by the Syrian position, and we said that we do not support the conference. We expressed our opinion clear and open," Shariatmadari told the paper, adding that the conference was a "a plot against the Palestinians."
Syria has said it decided to send its deputy foreign minister, Faysal Mekdad, to the summit only after the issue of the Israeli-occupied Golan Heights was added to the agenda.
Iran has been sharply critical of the conference, saying it was doomed to fail. But Shariatmadari's comments were the first from Iran that explicitly mention Syria's decision to participate.
U.S. officials are hoping Annapolis could mark a start to moving Syria out of its alliance with Iran and the Hamas and Hezbollah militant groups. But Syria has been cautious though so far, sending Mekdad instead of the country's top diplomat as other Arab countries have done.
On Monday, dozens of hard-line Iranian students gathered in front of the Jordanian Embassy in Tehran to protest the summit after Khamenei said in a speech broadcast on state TV that the summit was a failure meant to salvage America's reputation and not designed to help the Palestinians.
"Those who recognize Israel commit treason against Muslims and Palestinians," the protesters said in a statement in an apparent reference to Arab leaders who attended the conference.
On Tuesday, Iranian government spokesman Gholam Hossein Elham called on Arab and Muslim countries not to compromise with Israel at the Annapolis summit.
"Compromise in Annapolis will have no result except discrediting. It will damage the reputation of the U.S and its supporters," Elham was quoted as saying by the official news agency, IRNA. He said Iran might host a conference of Palestinian groups soon.
The official Iran daily newspaper also condemned the conference.
"Will Arab leaders be ready to compromise over rights of Palestinian nation against Palestinians?" Iran said in an editorial. "The Annapolis conference is nothing more than a ridiculous intervention maneuver in and inter-Palestinian dispute."
Elham also urged Muslim countries not to show their support for the Jewish state.
"Regarding our brotherhood relations with Islamic countries, such as Saudi Arabia, we are not interested in these countries standing next to the U.S. and Israel," IRNA quoted Elham as saying.
Nearly 50 nations and organizations are set to attend the summit to relaunch the long stalled Middle East peace process. Iran is not among the invitees.