Irbil, Iraq — Iraqi forensic teams uncovered the bodies Tuesday of at least 40 victims of last year’s massacre near Tikrit of government soldiers captured by the Islamic State group in the early days of its onslaught across northern and central Iraq.

And those graves are only the beginning. More than 1,000 Shiite Muslims are thought to have been killed after they were captured last year; the bodies of many now can be unearthed from the unmarked graves where they were dumped.

But the recapture of Tikrit last week after a bloody monthlong campaign also has revealed new abuses that add to Iraq’s nightmare — by the mostly Shiite Muslim security forces and their Shiite militia allies, even by Sunni Muslim allies of the government, against Sunni residents they accuse of backing the Islamic State.

All the bodies found Tuesday had been bound and shot in the head. An officer at the Salahuddin provincial command center outside Tikrit said the process of uncovering the hundreds of victims of last year’s killing will take “weeks or even months.”

“We’re not sure how many sites there are yet to be discovered,” he said, agreeing to speak only anonymously because of the sensitivity of the subject.

So far, government investigators have found at least three mass graves holding victims slain after the Islamic State captured hundreds if not thousands of members of the government security forces as well as poorly trained volunteer Shiite militias. The prisoners were forced to lie on the ground and were summarily executed at Camp Speicher, a one-time American military base, or shot in the head and tossed in the nearby Tigris River.

The Islamic State proudly documented the killings in online videos and magazine articles. The advocacy group Human Rights Watch later determined that at least 1,000 men were taken prisoner and at least 800 were quickly executed in what is considered the single worst mass killing of the current Iraqi civil war.

With Tikrit back in government hands, however, now it’s the government’s allies who are under investigation, accused of widespread looting and prisoner executions.

As security forces took control last week, journalists and civilians returning to the area witnessed widespread looting by both security forces and militias. Two local staff members from the Reuters news agency witnessed the summary execution of an Egyptian man accused of being an Islamic State fighter by a crowd of angry Iraqi policemen.

Concern about Shiite militia behavior as they moved into a Sunni area was one reason the United States withheld air support from the operation until Prime Minister Haider al-Abadi gave assurances that the militias would not enter the city itself as part of the final push. But the militias had a heavy presence in the town after its liberation and were seen openly looting government buildings and private homes, as well as burning buildings belonging to suspected collaborators.

Responding to public criticism, al-Abadi has announced that most of the Shiite militias would withdraw from Tikrit to begin operations in Anbar province, west of the capital, Baghdad. He pledged that anyone who engaged in revenge killings or looting would be arrested, although the government’s ability to arrest members of the powerful and militarily necessary militias is uncertain at best.

Amnesty International, the London-based human rights group, announced Tuesday it was investigating reports that government forces and their militia allies had committed abuses as the city fell.

“We are very concerned by reports of widespread human rights abuses committed in the course of the military operation in the area around Tikrit,” the rights watchdog’s Donatella Rovera told the AFP news service.

“We are investigating reports that scores of residents have been seized early last month and not heard of since, and that residents’ homes and businesses have been blown up or burned down after having been looted by militias,” said Rovera, a senior crisis response adviser at Amnesty.

“There have also been reports of summary executions of men who may or may not have been involved in combat but who were killed after having been captured,” she said.

One major Sunni tribe, the Jabour, also has been implicated in alleged abuses. Members of the tribe, among the first, if not the only, major Sunni clans to have joined the government offensive, are accused by some witnesses of having committed abuses as they helped the government retake their hometown of al Alam, a Tikrit suburb.

The officer at the Salahuddin command center said that allegations against the Jabour tribe involve local police who burned dozens of homes in both Tikrit and al Alam when they were able to return.

“There was heavy damage to the city and the surrounding area in the campaign to liberate Tikrit from Daash,” said the official, using an Arabic acronym for the Islamic State. “As the local police returned to the scene — these are people who know the area and know who collaborated with Daash and where their homes are — they took their revenge to ensure these traitors could not return.”

The Jabour tribe has long been an opponent of the Islamic State and its predecessor group, al-Qaida in Iraq, and has suffered heavy casualties over the past decade from attacks and suicide bombings of its members, said the officer, who described the tribes’ response to returning to Tikrit as “normal.”