Iraq's higher education minister has said he fears some ministry workers kidnapped by gunmen on Tuesday have been tortured and killed.
There is tight security around academic premises in Baghdad
Abd Dhiab said up to 80 remained in captivity, while some of those who had since been released were badly beaten.
They were among scores of workers taken hostage when the gunmen raided an education ministry building in Baghdad.
In continuing violence, gunmen killed nine people in an ambush on a bakery in the east of the capital.
The government has issued an arrest warrant for the country's most prominent Sunni cleric.
Interior Minister Jawad al-Bolani told Iraqiya state TV the head of the Muslim Clerics Association Harith al-Dari was accused of "supporting terrorism".
In an interview with the BBC, Mr Dhiab said he was "very much concerned" for the remaining captives' well-being.
He said there were "rumours and reports that some of them have been killed, even a number of those who have been freed were treated very badly, some of them had their legs and hands broken".
Mr Dhiab said between 70 to 80 people taken from the higher education ministry research facility were still missing, and that about 70 have so far been released.
"I hope all the hostages will be released as soon as possible. These are human beings and they should be released," he said, adding that the latest crisis was "a messy situation".
The Iraqi prime minister's office, however, has said that out of a group of 40 hostages, no more than five are still being held.
There has been tight security around universities and other institutions since Tuesday's raid, the latest in a series of attacks against Iraq's academic community.
Mr Dhiab has said he will suspend co-operation with the government until the remaining hostages are released.
"I am stepping down until something is done actively [to improve security], not just talk," he said.
'Pools of blood'
In continuing bloodshed in Baghdad, police said gunmen opened fire on customers and workers in the bakery in the religiously-mixed neighbourhood of Zayouna.
Most bakeries in the capital are run by members of Iraq's Shia majority and are frequently targeted by Sunni militants.
Funerals have already been held for victims of the bakery attack
The attack left pools of blood on the floor as people tried to flee in panic.
"The gunmen stormed into the bakery and killed workers while they were baking. They had done nothing bad," the Associated Press news agency quoted an unnamed man outside the store as saying.
In other violence, at least three civilians were killed in two explosions elsewhere in the capital.
A bomb attached to a motorcycle exploded in the Amal neighbourhood, killing at least one person, while a blast on Palestine Street in the east of the city killed two others.
The US military also announced the deaths of four of its soldiers in Iraq.
Two were killed by a roadside bomb and another was killed in action in north-east Diyala province on Wednesday; a fourth died in an operation in Baghdad on Tuesday.