Syria released 2,139 Syrian civilians in exchange for the return of 48 Iranians held by rebels, Hurriyet Daily News reported.
Bulent Yildirim, head of the Humanitarian Relief Foundation, who was overseeing the exchange in Damascus, said no one had received "any clear information" on Palestinian journalist Bashar al-Qaddumi, and observers were trying to determine his whereabouts.
The Turkish charity organization has been involved in other prisoner swaps in Syria.
The released prisoners were given money for travel expenses, Yildirim said.
A Syrian rebel spokesman said Wednesday's swap could be the biggest prisoner exchange the rebels have conducted with the government since the start of the conflict in March 2011, CNN reported.
"I myself went to two exchange negotiations," said Louai Miqdad, a spokesman for the rebel Free Syrian Army. "This is bigger."
In Douma, Syrian rebels released 48 Iranians, Iranian state television reported.
Miqdad said the Iranians released were part of a group abducted by rebels in last August. Iran has denied rebel claims the captives were members of Iran's Revolutionary Guard, countering they were Shiite pilgrims visiting a holy site in the Syrian capital.
Opposition leaders accused Syrian President Bashar Assad and his regime of caring more about releasing a few dozen captives from its ally, Iran, ahead of the release of thousands of government forces thought to be in rebel custody, CNN said.
"One Iranian person means more to him than a thousand soldiers," Miqdad said. "The command came direct from Tehran."
"The big prize for the regime is the Iranians, keeping them happy," said George Sabra, vice president of the National Coalition of Syrian Revolutionary and Opposition Forces. "The regime never cared about the lives of the civilian population or even [its] own armed forces."
Lakhdar Brahimi, the joint U.N.-Arab League envoy on Syria, told the BBC he thinks the Syrian people are saying a family ruling for 40 years is a little bit too long."
"The time of reforms granted magnanimously from above has passed," Brahimi said. "People want to have a say in how they are governed and they want to take hold of their own future."
Brahimi is scheduled to meet Friday in Geneva, Switzerland, with U.S. and Russian officials on Syria, The Daily Telegraph in London reported Wednesday.
The Syrian Network for Human Rights reported 77 people killed across the country Wednesday, the largest numbers in Aleppo, Damascus and its environs, and Hama.