The alleged confession was aired at a Baghdad press conference on Sunday
Iraq and Syria have both recalled their ambassadors in a deepening rift over claims Damascus was harbouring militants who bombed Baghdad.
Baghdad summoned its envoy home two days after airing a taped confession that linked two Syria-based Iraqi Baathists to a recent bombing campaign.
Hours later Damascus said it was bringing back its envoy in retaliation.
The two Arab neighbours only revived diplomatic links in 2006, after more than 20 years of mutual hostility.
Near-simultaneous bomb attacks last Wednesday at the finance, foreign and defence ministries in the heart of Baghdad killed nearly 100 people.
The taped confession of a man identified as Wissam Ali Kadhim Ibrahim said a Syrian-based Baathist leader, Sattam Farhan, ordered the attacks. It is impossible to verify the claims.
Correspondents say the flare-up throws extensive international efforts to boost ties between the countries for the sake of regional security and stability into disarray.
"Syria categorically rejects the statement of the spokesman of the Iraqi government regarding the bloody attacks in Baghdad last Wednesday," a foreign ministry said.
"Syria had forcefully denounced this terrorist act which left victims among the Iraqi people," it added.
Earlier, an Iraqi cabinet statement had called on Syria to hand over Mr Farhan and the other alleged mastermind, Mohammed Younis al-Ahmed.
"The cabinet decided to ask that they be handed over for their direct role in carrying out the terrorist operation," it said.
Syria is ruled by a rival branch of the Baath party, which was overthrown in Iraq by the US-led invasion and subsequently banned.
Hundreds of former Baathists are thought to have taken refuge in Syria since the 2003 collapse of Saddam Hussein's government.
In a separate development that appeared to run counter to the confession, a statement from an extremist Islamist militant group, that is violently opposed to the secular Baathists, has claimed responsibility for the attacks.
The Islamic State of Iraq, known to be an al-Qaeda umbrella group, said it had carried out the bombings to "wreck the bastions of infidelity" in Baghdad.
The statement was posted on Tuesday morning on a website commonly used by extremist militant groups.