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Demonstrators leveled harsh charges against the government.
"The injustice has reached its highest levels," said one demonstrator, who gave only his nickname, Abu Nouri, for security reasons. "Nouri al-Maliki is doing nothing for Iraqis," he said. "He's only busy removing political rivals from his path in the name of democracy and law."
"Why doesn't al-Maliki go after criminals and outlaws among the Shiites who sit in parliament and government, and are well-known for their atrocities over the years?" said another protester, who called himself Abu Omar al-Falluji, using a nickname for security reasons. "The answer is clear. He wants to shut the mouths that criticize him to turn this country into a pure Shiite one affiliated to Iran," he charged.
Fallujah, a former insurgent stronghold, is located 65 kilometers (40 miles) west of Baghdad.
The case of al-Issawi will likely fuel the simmering political infighting over power sharing in post-Saddam Iraq.
On Friday, Sunni Deputy Prime Minister Saleh al-Mutlaq threatened that his Iraqiya bloc could withdraw from the political process altogether if lawmakers and independent bodies are not allowed to monitor the investigation involving al-Issawi's staff.
The arrests came a year after the government arrested nearly 70 bodyguards assigned to Sunni Vice President Tariq al-Hashemi on terrorism-related charges. Then al-Hashemi himself was convicted of orchestrating death squads, a charge he dismissed as politically motivated.
Iraqi courts have since handed down multiple death sentences against him. He now lives in neighboring Turkey.
Associated Press writer Sinan Salaheddin in Baghdad contributed.