Announcing the amnesty for tribesmen who have not killed Iraqi forces, al-Maliki said, "I welcome them back to the fold and to rejoin their brethren in other Iraqi tribes."
He also strongly rejected the Kurdish regional government's effective annexation of the disputed oil-rich city of Kirkuk and other areas in northern Iraq, saying it was unacceptable.
He called on the Kurdish leaders not to take advantage of the state's current weakness to advance their own specific agendas. Any attempt to hold a referendum on the move is invalid because there is no provision in the constitution for self-determination, al-Maliki added.
The Prime Minister did not say how he planned to address the move.
Kurdish leader Masoud Barzani announced Friday that the disputed areas, including Kirkuk, were henceforth part of the Kurdish autonomous region, after the Iraqi central government failed to hold a long-awaited referendum.
Last month, the Iraqi army withdrew from Kirkuk and Kurdish Peshmerga forces took control of the city and small villages in the areas as ISIS carried out its lightning offensive.
The move by the Kurds will probably complicate efforts to get Iraqi lawmakers to form a new government representing all three major population groups -- Sunnis, Shiites and Kurds.
U.S.: Iraqi military probably would fight for Baghdad
Emboldened by the weakened Iraqi government's struggle to mount an effective response to their advance, ISIS extremists declared over the weekend that they had set up a caliphate -- or Islamic state -- spanning large areas of Iraq and Syria.
Iraqi military units around Baghdad are likely to stand and fight if ISIS militants attack the city, preliminary reports from U.S. military advisers in Iraq and U.S. intelligence personnel concluded, according to a senior U.S. official.
The U.S. assessment comes as intelligence also shows that Iranian Quds forces are increasing their efforts to train Shiite militias in and around Baghdad and in southern Iraq.
This assessment that Iraqi forces will fight for Baghdad is crucial to the U.S. need to keep Baghdad International Airport secure. The official says 300 American troops there now, along with several Apache helicopters, could not on their own secure the airport, crucial if an evacuation was needed, and it would require the Iraqis to devote a large number of their troops to the effort.
Iraq's military spokesman, Maj. Gen. Qassim Atta, told a news conference in Baghdad on Wednesday that the current military situation was going in favor of the country's security forces.
Atta said Iraqi forces have gained more ground from ISIS militants, many of whom have been killed or arrested.
In Salaheddin province, Iraqi forces have secured all the roads leading to the city of Tikrit, Atta said, and have retaken control of a military base formerly known as Camp Speicher on the outskirts the city, the hometown of ex-leader Saddam Hussein. Meanwhile, in Anbar province, they have killed 24 militants and arrested 11, among them a known ISIS leader and several of his aides, he said.
CNN cannot independently confirm his claims or reports of casualties.
Police officials in Samarra, in Salaheddin province, told CNN that the Iraqi air force struck several areas in the town of al-Shirqat, about 280 kilometers (170 miles) north of Baghdad on Wednesday.
At least 17 people were killed, including seven members of one family, while nine others were injured, officials said.
It was not immediately clear what the Iraqi air force was targeting.
Clashes at cleric's office
In unrelated violence, at least three people were killed Tuesday night when Iraqi security forces clashed with supporters of a radical Shiite cleric, police and health officials said.
Officials said Iraqi forces raided the offices of cleric Mahmoud al-Hassani al-Sarkhi in Karbala and clashed with his supporters. Nine people were wounded, and one military Humvee was set on fire, police said.
The fighting continued Wednesday, an employee at a shrine and a resident of Karbala told CNN.
Helicopters fired a number of times on the Saif Saad neighborhood, not far from the city's famed holy shrines, on Tuesday night, they said. The aircraft again hovered over the area Wednesday, as the city was placed on high alert and the streets remained empty of civilians.
Iraqi security forces have boosted security around the shrines and at the main entrances to Karbala.