The arrests of the three linked to Izzat Ibrahim al-Duri came as the US signalled its intention to disperse a designated Iranian "terrorist" group despite Tehran's objections.
"We detained three individuals in the extremist religious organisations with ties to ... Izzat Ibrahim al-Duri," Lieutenant Colonel William Adamson, head of the US task force in Baquba, said on Tuesday.
Al-Duri, who has a $10m bounty on his head, is number six on the list of 55 Iraqis most wanted by the United States.
He is alleged to be directing the resistance and is one of the top former Iraqi officials still wanted on the so-called American list of 55 displayed on a deck of playing cards.
Adamson said the arrested men also had links to central
Iraqi cities that are the fiercest areas of anti-American
resistance - Baquba, Falluja and Ramadi.
The arrests, part of raids in Baquba over the last 24 hours,
also netted another important four-member cell, Adamson said.
Meanwhile, Yusuf Khushi, a chief investigating judge in the northern city of Mosul, was shot and killed by three men in a car on Monday night, Iraqi police said on Tuesday.
Tensions have been high in Mosul,
scene of recent shootings
"He was shot six times from behind in the back. He died immediately," police Major Ali Muhammad said.
The slaying was part of a wave of attacks in recent weeks on officials working under Iraq's US administration, including policemen, oil executives and other judges.
Resistance guerrillas have killed US soldiers and anyone seen cooperating with them.
In a separate incident in Mosul, a US soldier was wounded in a drive-by shooting on Monday, said a spokesman for the 101st Airborne Division.
A car sped by and opened fire on a military foot patrol, Major Hugh Cate said on Tuesday.
Meanwhile, Iran has reacted angrily to remarks by Washington's Iraq overseer Paul Bremer that People's Mujahidin members would not be expelled to Iran but sent to third countries.
"If the US provides safe havens for them (mujahideen), they will not only further promote terrorism, but also violate the articles of the UN Security Council Resolution 1373, which is a dangerous precedent"
The group is named on the US' own list of designated terrorist organisations.
The Iranian foreign ministry summoned the Swiss ambassador, who heads the US interest section in Tehran, to express its protest about Bremer's statement.
Iran was "deeply concerned about the aftermath of such irresponsible remarks," the ministry's director general of American Affairs, Muhammad Hasan Fadaii Fard, was quoted by newspapers on Tuesday as telling Swiss envoy Tim Guldimann.
"If they provide safe havens for them, they will not only further promote terrorism, but also violate the articles of the UN Security Council Resolution 1373, which is a dangerous precedent that can be taken advantage of by other supporters of international terrorism."
On Monday, Iran's reformist President Muhammad Khatami proposed members of the Iraq-based People's Mujahidin, the main Iranian armed opposition, return home, promising they would be treated with leniency.