The stepped-up covert mission supporting Iraq's Counter-terrorism Service, or CTS, targets al-Qaida in Iraq, also known as al-Qaida in Mesopotamia, a Salafi jihadi militant al-Qaida affiliate that is part of the Iraqi insurgency.
U.S. intelligence agencies believe the al-Qaida group is providing a steady stream of fighters to battle for Syria's al-Nusra Front, also called Jabhat al-Nusra, an opposition militant group that has attacked Assad regime installations and controls parts of northern Syria, the Journal said.
The State Department placed al-Nusra on its list of foreign terror organizations in December, calling the group an alias for al-Qaida in Iraq.
The White House directed the CIA to support CTS -- an elite anti-terrorism group that reports directly to Iraqi Prime Minister Nouri al-Maliki -- in a series of secret decisions from 2011 to late 2012, the Journal said.
The CIA has since ramped up its work with the CTS, taking over a mission long run by the U.S. military, administration and defense officials told the newspaper.
U.S. Special Operations Forces previously worked with CTS against al-Qaida in Iraq. But the U.S. military role has dwindled since U.S. troops pulled out of Iraq at the end of 2011.
The Journal said the increased use of the CIA in Iraq was in line with the Obama administration's goal of limiting the U.S. role in the Syrian conflict.
The administration is providing non-lethal assistance to the opposition, but says it won't send weapons, in part to avoid helping extremist elements among rebel forces.
The White House had no immediate comment.
Syrian violence is increasingly spilling into Iraq.
About 50 Syrian soldiers who had sought safety in Iraq from rebel fighters were killed last week in an ambush in Iraqi territory. Baghdad said the attack had the hallmarks of an attack by al-Qaida in Iraq.