The abductions from the Sunni-controlled ministry were carried out by men wearing uniforms that had been newly designed for interior ministry police commandos.
This has prompted claims that the Iraqi police are working with armed Shia groups and Dhiab has called it a "sectarian attack".
Some hostages were freed on Wednesday, but there is confusion over how many were originally taken, how many have since been released and the number still being held.
Dhiab said that 150 staff and visitors were originally seized and that about 70 were released on Wednesday.
But the office of Nuri al-Maliki, the prime minister, said that only 40 had been taken on Tuesday and that no more than five were still missing.
Dhiab said that the hostages were taken to a stronghold of armed Shia groups in Baghdad.
A higher education ministry spokesman said officials were compiling a list of names of those seized.
He said it included the names of at least 100 employees of two departments in the building, as well as about 50 visitors. Dozens remain unaccounted for.