There is mounting concern among scholars that the appointment of religiously conservative Shiite Muslims throughout Iraq’s traditionally secular archaeological institutions could threaten the preservation of the country’s pre-Islamic history.

Donny George’s recent departure as chairman of the State Board of Antiquities and Heritage, and his flight to Syria with his family, is among the latest results of a transformation that began in December when a Shiite-dominated government was elected in Baghdad.

The radical Shiite cleric Moktada al-Sadr, who commands his own militia, emerged with enough seats in Parliament to take control of four ministries and to create a Ministry of Tourism and Antiquities.

The State Board of Antiquities and Heritage, traditionally under the Ministry of Culture, now reports to this new ministry as well.

"The Ministry of Tourism and Antiquities wants to control Iraq’s archaeological heritage by demolishing this institution, one of the oldest institutions in Iraq," Dr. George said in a telephone interview from Damascus. "This will be a disaster for this field, and for the cultural heritage of the country."

Although the Ministry of Tourism and Antiquities has begun operating, the law creating it has not yet been approved by Parliament, which is about to begin debating the measure, said Abudul Zahra al-Talaqani, a spokesman for the new ministry.

The proposed law would divide the State Board of Antiquities and Heritage into four administrative departments: museums, excavations, manuscripts and heritage. The present departments of restoration and research would be eliminated, suggesting that preservation and scholarship would no longer be the institution’s focus.

The long history of secular scholarship in Iraq has covered all periods, including excavations at the Islamic site of Samarra and the restoration of Ukhaidir, an Islamic fortress near Karbala. Earlier sites include ruins from the Sumerian, Akkadian, Babylonian, Parthian and Sassanian civilizations.

The State Board of Antiquities and Heritage was created in 1923, when Gertrude Bell, the British explorer and administrator, founded the Iraqi National Museum. "It was the best in the whole Middle East," said McGuire Gibson, a professor of Mesopotamian archaeology at the University of Chicago. "At one point there were 13 Iraqi Ph.D.’s working there."

Liwa Sumaysim, the new minister of tourism and antiquities, is a dentist whose wife, a member of Parliament, is related to Mr. Sadr. The new ministry has already replaced employees of the State Board of Antiquities and Heritage at both the national and local level.

Burhan Shakur, an archaeologist who was director of excavations at the Iraqi Museum, was fired in the spring, then given the option to retire; he has left for Germany. Abdul-Amir Hamdani, the inspector for antiquities in the Dhi Qar province, an area rich in pre-Islamic sites, was jailed in April on charges of corruption. After three months he was released, and the charges were dropped. But his job was then filled by a man with ties to Al Fadilah, an Islamist party aligned with the Sadr movement.

With the looting of archaeological sites in southern Iraq still thriving, control of the antiquities department is a significant prize. Most of the archaeological sites in the southern Dhi Qar province are pre-Islamic, dating roughly from 3200 B.C. to A.D. 500.

A link between Islamic militants and looting at pre-Islamic archaeological sites has long been suspected, but is difficult to prove. The Nasiriyah Museum was burned and looted in 2004 by militants affiliated with Mr. Sadr. The museum’s guards reported that the militants promised to do to the antiquities there exactly "what the Taliban did."

The center for Iraq’s illicit antiquities trade, Fajr, in the heart of the Sumerian plain, is also a stronghold for militants loyal to Mr. Sadr. And anti-Western graffiti has appeared at looted archaeological sites.

"It is hard to say yes or no if these gangs have a relation with the Sadr movement," cautioned Mufeed al-Jazairi, Iraq’s first minister of culture after the Coalition Provisional Authority disbanded, who noted that looters were active in Saddam Hussein’s time as well. "But it is not surprising to imagine that one of these gangs will announce that they are allies with Sadr, hoping to gain a political shield in case they are being followed by authorities."

The recent deployment of a 1,400-strong Mobile Archaeological Site Protection Force was considered a hopeful sign by scholars. The guards, in an effort conceived in 2003, finally began work in November 2005. They were first used in Dhi Qar under the direction of Mr. Hamdani.

"Now there is no money to pay them beyond August," Dr. George warned last month. "I had been applying for money to protect the guards in the south, and I never got that money. There was money allocated to different Islamic projects."

Mr. al-Talaqani, the ministry spokesman, denied that there was a lack of funds for the mobile guard force. "The government is concerned with protecting all cultural history in all regions," he said. But reports from the south indicate that there is no money for fuel and that the patrols have stopped.

"If the destruction of sites continues, it is not just the death of archaeology," Dr. Gibson of the University of Chicago said. "Antiquities are key to Iraq’s economy; at some point the oil will run out. Iraqi tourism will be built on archaeology."

Yet Dr. Gibson warned that putting an archaeological department under a tourism office tends to have negative consequences because sites may become mothballed, and research possibilities lost.

The Sadrist leadership in the new ministry has made its views known in other ways. Recently two pre-Islamic statues it returned to the Iraqi Museum were accompanied by a note describing them as "idols." Elizabeth Stone, an archaeologist and professor of anthropology who has excavated in southern Iraq, said that officials of the Ministry of Tourism and Antiquities had also visited the museum before the departure of Dr. George, who is Christian, and asked, "Do you want to be governed by a crusader?"

Dr. Stone, who is now training Iraqi archaeologists at Stony Brook University, joined others in the archaeological and diplomatic communities in praising Dr. George. "As director general, he was really fighting for Iraqi antiquities," she said. "He had a vision for where international archaeology could go, particularly in collaborating with other institutions. That is all gone."

Dr. Gibson, who worked at the Nippur archaeology site in Iraq, agreed. "The loss of anyone with the qualifications and dedication he has to the archaeology of Iraq is really a tragedy," he said. "We would hope he would stay on, but he is one of many leaving the country."

From Damascus, Dr. George suggested that hope for Iraq’s cultural heritage lay with Mr. al-Jazairi, the former culture minister, and his former deputy, Naysoon al-Bamaluji, who are now in Parliament; the current minister of culture, Afad al-Hashimi;and those working in the provinces.

"We need to rehabilitate the Iraqi Museum and make people aware of the importance of archaeological artifacts," Mr. al-Jazairi wrote in an e-mail message from Baghdad, "and to make strict procedures to stop the sabotage of archaeological sites."

MICAH GAREN and MARIE-HÉLÈNE CARLETON