The accusations would also seem to dampen the prospect of reconciliation that the United States, the U.N. and even Iraq's top Shiite cleric say is necessary to bridge the country's ethnic and sectarian divisions and hold Iraq together.
The militant offensive spearheaded by the Islamic State extremist group has plunged Iraq into its worst crisis since the last U.S. troops left the country in 2011.
The jihadis have been joined in their assault by other Sunni insurgents, feeding off the anger in their minority community against the Shiite-led government. On the other side, Shiite militias have rallied around al-Maliki's government to fight off the insurgents.
In the far north, meanwhile, Iraq's Kurds have taken advantage of the mayhem to seize disputed territory including the city of Kirkuk, a major oil center and move closer to a long-held dream of their own state.
The Kurds say they only want to protect the zones they have entered from the militants, but many of the areas have significant Kurdish populations. The Kurds also have allowed tens of thousands of civilians into the Kurdish-controlled areas to escape the militant onslaught.
Last week, the president of the Kurdish area urged the region's lawmakers to move quickly on preparations for a referendum on independence.
These moves have infuriated al-Maliki, who is under pressure from opponents as well as former allies to step down.
Speaking Wednesday, al-Maliki took aim at the Kurds, whose regional government is based in Irbil, saying, "Everything that has been changed on the ground must be returned."
He went a step further, saying: "We can't stay silent over Irbil being a headquarters for Daesh, Baath, al-Qaida and the terrorists." Daesh is the acronym in Arabic for the Islamic State group, while Baath was the party of former dictator Saddam Hussein.
A spokesman for the Kurdistan Regional Government, Safeen Dizayee, called al-Maliki's accusations "baseless."
"The Kurdistan region has never harbored any terrorists, now or ever, because we have been the victim of them before," Dizayee said. "What Mr. al-Maliki is talking about is far from reality."
Al-Maliki provided no evidence to back up his claims, and there is no indication that Baathists or Islamic extremists are operating openly out of Irbil.
But tribal sheiks who oppose the central government whose fighters are battling the military have found refuge in the Kurdish capital.
One of the anti-al-Maliki sheiks, Abdul Razzaq al-Shammari, told The Associated Press that "Kurdistan is not hosting any terrorists though there are people here who stand against the Iraqi political regime."
The militant offensive has dramatically raised tensions between the country's Shiite Arab majority and Sunni minority, and the discovery of the 50 bodies raised the specter of sectarian massacres.
The bodies were found in the predominantly Shiite village of Khamissiya, about 95 kilometers (60 miles) south of Baghdad, said military spokesman Brig. Gen. Saad Maan Ibrahim. He said an investigation was underway to determine the identities of the dead and the circumstances of the killings.
The dead were all men between the ages of 25 and 40, and it appeared they had been killed a few days earlier and then dumped in the remote area, said a local police officer and a medical official.
Most of the bodies had bullet wounds in the head or the chest, they said on condition of anonymity because they were not authorized to speak to the media.
The area is predominantly Shiite, but there is a belt of Sunni-majority towns to the north.
Such killings harken back to the worst days of Iraq's sectarian bloodletting in 2006 and 2007.
Sectarian tensions have soared once more since the Sunni insurgent blitz began last month, and authorities have once again begun to find bodies.