Police Brigadier Abd al-Karim Khalaf said the charges marked the first time officers in Iraq's post-invasion police force had been charged with the crime of torture.
The names of the accused are being withheld until their trials, but Khalaf said the general had already been under the police force's guidelines.
Others charged included 19 officers, 20 noncommissioned officers and 17 patrolmen or civilian employees of the ministry, he said. All have been removed from their jobs.
"All of these people will stand trial and the court will decide their fate," Khalaf said.
The charges are the first to be brought against high-ranking police officers over allegations of torture, reported to be widespread among the poorly trained force.
Last year, a police torture chamber was discovered in Baghdad, and this October an entire brigade of about 700 policemen was suspended from service and returned to its barracks because of suspected complicity in a mass kidnapping of Sunni workers.
Iraqi detainees are often held in overcrowded cells with little sanitation, while alleged abuses include starvation and beatings.
Officials say they plan to eventually retrain all 26 national police battalions - the interior ministry's paramilitary units - and identify those with ties to sectarian militias and criminal gangs.
Many Iraqis are enraged by reports of detainee torture and other abuses in prisons run by the US military after the 2003 invasion that toppled Saddam Hussein, the former president.