Jack Healy reports from Baquba: The governor has fled this uneasy city. Half the members of the provincial council are camped out in northern Iraq, afraid to return to their offices. Peaceful protesters fill the dusty streets, though just days ago angrier crowds blockaded the highways with burning tires and shattered glass.

All of this because the local government here in northeastern Diyala Province recently dared to raise a simple but explosive question, one that is central to the unrest now surging through Iraq’s shaky democracy: Should a post-American Iraq exist as one unified nation, or will it split into a loose confederation of islands unto themselves?

A dire political crisis exploded in Baghdad this week, after an arrest warrant was issued against the Sunni Arab vice president, Tariq al-Hashimi, accusing him of running a death squad. But years of accumulated anger and disenfranchisement are now driving some of the country’s largely Sunni Arab provinces to seek greater control over their security and finances by distancing themselves from Iraq’s Shiite leaders.

Many Sunni leaders have rallied to the cause while top Shiites in Baghdad have fought the efforts, aggravating the sectarian divisions among the country’s political elite.

“They feel that they have no future with the central government,” said Deputy Prime Minister Saleh al-Mutlaq, a prominent Sunni.

This development comes at a moment of rising tensions and could herald a near-breakdown of relations between the countryside and the leaders behind the concrete walls and concertina wire guarding Baghdad’s Green Zone. It has splintered communities within provinces along religious lines, while deepening the sense of political uncertainty pervading Iraq in the days after the American military’s withdrawal.

“We’ve reached a point where the exasperation with the entire political process is so big in Sunni majority areas,” said Reidar Visser, an expert on Iraqi politics and the editor of the blog historiae.org. “They are just fed up and disillusioned.”

On Friday, thousands of protesters marched through largely Sunni cities to condemn the warrant for Mr. Hashimi’s arrest. In Samarra, where the destruction of a Shiite shrine in 2006 set off waves of violence, 2,000 demonstrators filled the streets after Friday Prayer, waving signs that declared, “The people of Samarra condemn the fabricated charges against Hashimi.”

The schism is one thread of a growing battle between Prime Minister Nuri Kamal al-Maliki, a Shiite, and politicians from the political opposition and Iraq’s Sunni Muslim minority.

Security forces who take orders from Mr. Maliki — sometimes personally — have arrested dozens of people tied to opposition politicians in recent weeks. The government accused Mr. Hashimi, the Sunni vice president, of running a death squad from his offices in central Baghdad, a charge he denies. And Mr. Maliki has urged Iraqi lawmakers to unseat his own deputy, Mr. Mutlaq, who frequently inveighs against the prime minister.

A leading political coalition supported by many Sunnis and secular Iraqis has boycotted Parliament, refusing to attend sessions, and its ministers and lawmakers have threatened to resign en masse. An American-backed partnership government uniting Iraq’s three main factions — the Shiite majority, Sunnis and Kurds — appears poised to fall.