The killings were reminiscent of the situation in the city in 2006 and 2007 -- when the body count in Baghdad was at its highest -- and came as the invading Islamic State in Iraq and Syria (ISIS) overtook several neighborhoods in Baquba, about 40 miles from Baghdad.
"Everything in the city is now under control, and the groups of armed men are not seen in the city," said Brig. Gen. Jameel Kamal a-Shimmari, Baquba police commander, after what he said was a three-hour gun battle with the Sunni militants.
Gen. Qassim Atta, an Iraqi government spokesman, said the prisoners died when the police station was struck with ISIS artillery shells. However, a source at the city morgue said many of the victims had wounds that indicated they were shot at close range. An Internet statement by ISIS claimed the prisoners were executed by police.
The violence in Baquba is the closest to Baghdad that ISIS has come, after capturing the cities of Mosul and Tal Afar in the past week. Shiite residents are fearful of a renewal of sectarian violence; although Shiites control the Iraqi government, they are heavily outnumbered by Sunnis in Iraq.
"We are afraid of a massacre of the Shiite minority if the security situation collapses," said Jaafer al-Rubaie, a Baquba retired government official.
United Nations Secretary-General Ban Ki-moon expressed concern over reports of the killings Tuesday and urged Iraqi Prime Minister Nouri al-Maliki -- who has attempted to recruit civilian Shiites to defend Baghdad -- to engage in inclusive dialogue.