Some of those killed were shot dead on Saturday, when the militants moved into the towns, while others were slain the following day.
The killings came after Iraqi security forces members departed the towns, clearing the way for the militant takeover.
"The military units' withdrawal (from Rawa and Ana and Al-Qaim) was for the purpose of redeployment," Lt Gen Qassem Atta said, referring to it as a "tactical" move.
Witnesses said insurgents moved into Rawa and Ana, in Anbar province, on Saturday evening, after security officers and witnesses also reported militants entering Al-Qaim, a town on the Syrian border, earlier in the day.
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Beginning late on June 9, militants led by the Islamic State of Iraq and the Levant (ISIL) but also including a number of other groups such as loyalists of executed dictator Saddam Hussein, overran most of one province and parts of three others north of Baghdad.
The security forces wilted in the face of the initial onslaught, in many cases abandoning vehicles, equipment and even their uniforms.
They appear to have recovered in the past few days, with officials touting gains against militants, though insurgents have made territorial progress elsewhere.