Abu Raqeef denied the report, saying: "I am still in the ministry, carrying out my duties, and these accusations are baseless."
Another security official said a brigadier-general in the traffic police was the highest-ranking figure detained. Most are low-level ministry employees, he said.
Khalaf said the officers were arrested on suspicion of being part of the al-Awda (Return) party, a Sunni underground organisation founded in 2003 to try to restore the Baath party and Saddam Hussein, the president overthrown by US-led forces and later executed.
"They are now being interrogated under the supervision of the Iraqi judiciary," Khalaf said.
Asked whether they were plotting a coup, Khalaf repeated that they were suspected of being al-Awda party members.
Brigadier-General Alaa al-Taei, the ministry's head of public relations, said those arrested were not accused of plotting a coup, but were suspected of planning to burn down the ministry, possibly to destroy evidence against them.
Coup threat in doubt
Some Iraqi politicians said they doubted that the employees had been actively trying to overthrow the government.
Abbas al-Bayati, a legislator from the Supreme Iraqi Islamic Council, the largest Shia party, said: "I think talking about a coup is an exaggeration."
He described those arrested as "a semi-organised group", but said the fact that they were trying to restore the Baath party pointed to shortcomings in Iraqi security in Baghdad, the capital, and elsewhere.
Hadi al-Amiri, the head of the Iraqi parliament's security committee, told Associated Press Television News that reports of a coup attempt were "baseless".
"In fact, coups are usually carried out by the army and not by police," he said.
Mahmoud Othman, a Kurdish bloc legislator, said he hoped "the move against those arrested is not politically motivated or aims at electoral gains".
Also on Thursday, the speaker of the Iraqi parliament, Mahmoud al-Mashhadani, returned to the chamber a day after saying he was resigning.
Al-Mashhadani said he was resigning during a debate over the jailing of an Iraqi journalist who had drawn popular support after throwing his shoes at George Bush, the US president, during a Sunday news conference in Baghdad with Nuri al-Maliki, the Iraqi prime minister.
It was unclear at the time whether al-Mashhadani spoke out of pique or intended the statement as a formal announcement.
Salim Abdullah, a spokesman for the largest Sunni bloc in parliament, said that al-Mashhadani had been present for a parliament session on Thursday.