Exactly who these people were and why they were killed is not clear, but Col Qasim al-Obeidi said he believed some were members of the security forces.
IS fighters captured much of the town, near Ain al-Asad air base, last week.
Col Obeidi said a compound that houses the families of security personnel and local officials was now under attack.
He pleaded for help from the government and the international community.
The fighting and poor communications in the area make it difficult to confirm such reports.
Earlier this month, IS published a video showing militants burning alive a Jordanian air force pilot, whose plane crashed in Syria in December.
Al-Baghdadi had been besieged for months by Islamic State fighters before its fall on Thursday.
It had been one of the few towns to still be controlled by the Iraqi government in Anbar province, where IS and allied Sunni Arab tribesmen launched an offensive in January 2014.
Pentagon spokesman Rear Adm John Kirby told reporters on Friday that al-Baghdadi's capture needed to be put in perspective.
He said it was the first time in the last couple of months that the jihadist group had taken new ground.
|Ain al-Asad air base - does not look easy to defend|
The base was itself attacked by IS militants, among them several suicide bombers, on Friday. The militants were eventually repelled by Iraqi troops backed by US-led coalition aircraft.
The US needs to evacuate Ain al-Asad air base, and evacuate it quickly. Booby-trapping the place when they leave might also be a good idea. But there is little point in holding a base in the middle of IS territory, not when IS has started burning prisoners alive.
Shia militants withdraw from fight with IS
In a separate development on Tuesday, the influential Shia cleric Moqtada Sadr announced he was withdrawing his forces from an umbrella group of Shia militia fighting IS alongside the Iraqi army.
He cited what he called the bad behaviour of other militia within the Popular Mobilisation Forces, whom he accused of "wreaking havoc through murdering, kidnapping and violating sanctuaries".
Shia militia have been accused of kidnapping and killing scores of Sunni civilians since Islamic State launched an offensive in northern Iraq last June that saw it seize large swathes of the country.
Cleric Sadr didn't mention the bad behaviour of his own militants; it's always the other guys. But one has to wonder if the apparent new policy of prisoner immolation has affected the decision to pull his troops.
How do you fight an ideology that is based on utter madness? The first incident of IS burning prisoners alive sparked quick and dramatic response from the Jordanian air force, thereby bringing a powerful military against them. Yet they continue to escalate the practice.
The beheading of 21 Egyptian Coptic Christians in Lybia brought another powerful military against IS, yet the continue to slaughter at will.
There is little or no fear of death among the crazed, radicalized IS fighters. The fools actually think they will go straight to paradise when they die. But Hell is no paradise, and that is where those who have gone before are waiting for their lunatic brothers.