Baghdad has seen a proliferation in recent years of well -armed criminal gangs that carry out contract killings, kidnappings and extortion.
Some elements of powerful Shia armed groups, which are seen as a critical deterrent against Islamic State militants, have also been accused of kidnapping people for political or criminal purposes.
Read: Over 50 Turkish jets bomb PKK targets in northern Iraq
Security sources said another ministry official and two guards were also abducted. A ministry spokesperson declined to comment but identified the deputy minister as Abdel Karim Faris.
Last week, gunmen seized 18 Turkish construction workers from a sports stadium they were building in northeastern Baghdad.
Iraqi security forces investigating the incident later raided the headquarters of a powerful Iranian-backed Shia militia, but the workers are still missing.
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