Aljazeera quoted Bayan Baqir Solagh Jabir as saying that he will put on trial any official found guilty of beating or abusing detainees at his ministry.
He added that the number who were tortured at al-Jadriya bunker did not exceed seven out of more than 75 detainees.
The Iraqi deputy interior minister said earlier this week that the number was closer to 160.
"I don't accept for any officer to even slap a prisoner," Jabir told a packed news conference on Thursday, his first public appearance since US forces found the bunker and scores of malnourished and badly beaten men on Sunday.
"The talk about this has been inaccurate," he said, adding that he was commenting on the issue only because his aides had put pressure on him to do so.
Prime Minister Ibrahim al-Jaafari said earlier this week that 173 men and teenage boys were discovered at the prison near the Interior Ministry, and said there was evidence that many of them had been tortured. He has ordered an investigation.
Jabir, raising his voice in anger as he dismissed several of the allegations being made, said only a handful of people showed any sign of being beaten, and they were all detained for suspected violent activity after arrest warrants were issued.
Political leaders from Iraq's once-dominant Sunni Arab group have demanded an international investigation into allegations that Shia militias linked to the Interior Ministry were responsible for the torture and abuse.
Jabir angrily rejected most
accusations of torture
The head of the main Shia militia, the Badr Organisation, which has close ties to the Interior Ministry and to the most powerful Shia political party in the government, on Wednesday denied any involvement with, or link to, the detention bunker.
The discovery is likely to fuel sectarian tension between Iraq's Sunni Arab group and al-Jaafari's Shia and Kurdish-led government in the run-up to 15 December parliamentary elections.
Most of those found inside were Sunni Arabs, officials said.
Local and international media published gruesome accounts on Thursday of how some of the detainees were treated.
Mohammad Duham, the head of a group that works to protect prisoners and detainees, told Reuters torture implements had been found in the bunker, including saws to cut detainees' limbs and razors to peel off their skin.
"This is unacceptable and claims we used things to carve people's limbs are absurd," Jabir said.
He said Iraq abided by the Geneva Convention governing the treatment of prisoners of war and invited non-government organisations and the media to inspect any prison run by the interior ministry.
The Interior Minister says many
prisoners were 'terrorists'
He denied that Sunnis had been targeted by the ministry and said Shias were among the detainees, who were overseen by 29 officers assigned to the building, a concrete structure half below ground and half above.
All those detained had been the subject of arrest warrants,
he said. "They were all dangerous terrorists. They will get their justice through the judicial system," he said.
The abuse scandal has drawn local and international condemnation.
Call for probe
Speaking to Aljazeera from Baghdad, Iraqi Islamic Party member Iyad al-Izzi said: "We call for at least an international investigation to probe the abuse as we have not seen any interest from the Iraqi government in dealing with this issue.
"We have no confidence in this government after the disappointing performance we have seen recently", he said.
Iraq's interior minister says not
all the detainees were Sunnis
Meanwhile, a spokesman for the Association of Muslim Scholars, Abd al-Salam al-Kubaisi, has called for an international investigation in which the Iraqi government must not take any part, Aljazeera reports.
Speaking on Wednesday, he called on the Arab League to shoulder its legal and moral responsibilities in this matter.
For his part, Iraqi President Jalal Talabani said torture and humiliation were not welcome in the new Iraq, and condemned what he said was the crime that had been committed.
Aljazeera quoted Talabani as saying that those involved in the affair should be tried and punished regardless of their position.
US embassy reaction
Also on Thursday, the US embassy in Baghdad said violation of detainee rights and interference by militias in the arrest of suspects cannot be tolerated, and the same goes for domination of Iraqi security forces by militias and sects.
Addressing journalists, a spokesperson for the US embassy said the Iraqi government should take measures guaranteeing that detainees would not be abused in the future.
UN Secretary-General Kofi Annan, who visited Iraq at the weekend for the first time since the removal of Saddam Hussein in 2003, expressed concern but welcomed al-Jaafari's statement that such practices were contrary to government policy.