Sunnis, the minority Muslim sect in Iraq, feared a new round of sectarian warfare could result from the charges, announced the day after the last American soldiers left the country. The accusations date back to the height of the war in 2006 and 2007, when neighbors turned on neighbors and whole sections of Baghdad were expunged of one Muslim sect or the other.
Kurdish leaders were trying to work out a solution, sheltering al-Hashemi from arrest in their semiautonomous region in northern Iraq.
"I swear to God that al-Hashemi didn't commit any sin or do anything wrong against any Iraqi either now or in the future and this is my pledge to God," al-Hashemi said at a news conference in which he accused al-Maliki of ordering the warrant.
He described the confessions of his bodyguards that aired on Iraqi state TV as "fabricated" and the charges as a campaign to "embarrass" him.
"Al-Maliki is behind the whole issue. The country is in the hands of al-Maliki. All the efforts that have been exerted to reach national reconciliation and to unite Iraq are now gone. So yes, I blame al-Maliki," he said.
Al-Hashemi spoke from the Kurdish city of Irbil, where he traveled on Sunday after learning that authorities were preparing to arrest him.
Although the Kurdish region is part of Iraq, al-Hashemi is probably safe from Baghdad's reach. Kurdish leaders run their own security affairs. The Iraqi Army or national police do not travel there, and al-Maliki would be reluctant to ask the Kurds, a powerful political bloc that he needs, to return al-Hashemi for prosecution.
Most Kurds are Sunni Muslims, but they are a different ethnic group from the Arabs that make up the vast majority of Iraq's population.
Al-Hashemi said he might leave Iraq temporarily. He has often traveled to neighboring Turkey, and many lawmakers in his Sunni-backed Iraqiya political bloc have essentially made Jordan their second home.
On Monday, state-run television aired what it characterized as confessions by men said to be bodyguards for al-Hashemi. The men said they killed officials working in Health and Foreign Ministries as well as Baghdad police officers, and that they received $3,000 from al-Hashemi for each attack.
Al-Maliki effectively runs the Interior Ministry, where the charges originated. Iraqiya has repeatedly accused the Shiite prime minister of hoarding power and last weekend boycotted parliament because al-Maliki refused to give up control over key posts.
"The political process is on the brink of disaster because of the decisions made by the government in the past two days," said Jasim al-Halbusi, member of the Anbar Provincial Council. Anbar is dominated by Sunnis.
"There are some people who have to understand that Iraq cannot be ruled by one sect," he said, alluding to al-Maliki's Shiite allies.
Sunni politicians worried they could be next on the arrest list, and Sunni neighborhoods braced for the worst.
"The arrest warrant is a starting signal to get rid of any person who might pose a threat to al-Maliki's dictatorship," said Ibrahim al-Obeidi, a resident of the Sunni-dominated Azamiyah neighborhood of northern Baghdad. "The streets are almost empty. People fear the resumption of sectarian violence."
It was not immediately clear whether al-Hashemi's Iraqiya coalition would remain as part of the al-Maliki-led government. Iraqiya encompasses different factions with their own agendas.
Even if the bloc does pull out of the government, al-Maliki might keep enough support from other groups, especially the Kurds, to form a majority government. Or he could limp along with a minority government.
A U.N. spokesman, Martin Nesirky, said the Secretary-General Ban Ki-moon was following the political situation closely.
"He urges Iraqi political leaders to engage in inclusive and constructive dialogue to resolve their differences," Nesirky said.
White House press secretary Jay Carney said the Obama administration is "obviously concerned" about the case and is urging all sides to resolve their differences peacefully.
"We urge the Iraqi authorities charged with this responsibility to conduct their investigations into alleged terrorist activities in accordance with international legal norms and full respect for Iraqi law," Carney said.
There was no way to know whether there was any substance behind the charges against al-Hashemi. Some Shiite politicians have also been accused of nefarious acts but have not been charged.
Joost Hiltermann, an Iraq analyst at the International Crisis Group, said al-Maliki's campaign against al-Hashemi is driven by a genuine fear that there's a plot against him.
"These parties come out of exile and are dominated by fear of decimation by the former regime," he said. "They think they're all plotting against each other all the time."
While the American military was in the country, they were able to keep a lid on this paranoia and help bring the two sides together. But, Hiltermann said, with the Americans gone those fears are coming to the surface.
Al-Maliki is also deeply worried about what will happen in neighboring Syria, Hiltermann said. The government of President Bashar Assad, which is ruled by a Shiite offshoot of Islam, is battling an uprising that threatens to unseat him from power.
If Assad is ousted, many in Iraq's Shiite-dominated government worry that it could lead to the installation of a conservative Sunni regime in Damascus aligned with Saudi Arabia. That could even further deepen Iraq's sectarian problems.
Al-Maliki has made a series of moves in recent months to secure his hold on power. Hundreds of former members of Saddam Hussein's Baath Party have been rounded up, allegedly as security threats, although no proof has been given. In Tikrit, Saddam's hometown, arrests have become so commonplace that whenever a police car shows up, young men flee from the street.
The trial-by-television aspect of the case against al-Hashemi raised questions about the ability of the judicial system to prosecute the case fairly. Despite years of U.S.-funded training to bolster up their security forces, many American military commanders have quietly questioned Iraq's and especially al-Maliki's commitment to the rule of law.
Al-Hashemi said he was surprised by statements from President Obama praising Iraq's nascent democracy.
"As a vice president whose house is surrounded by tanks ... I deliver this question: What kind of democracy are you talking about, Mr. Obama?"
Associated Press writers Sameer N. Yacoub, Sinan Salaheddin and Mazin Yahya in Baghdad, Edith M. Lederer at the United Nations and Kenneth Thomas in Washington contributed to this report.