Eighty-four children, all Tajik citizens, had been "forced to join the ranks" of the militant groups after their parents were recruited, according to the statement on the ministry's website.
They returned on a special flight from Baghdad to Tajikistan's capital Dushanbe on April 30, it added.
In February Tajikistan's foreign ministry said it was seeking the repatriation of 75 children marooned in Iraq where 43 Tajik women are serving jail sentences for extremism-related crimes.
Repatriating the jailed women would be far more difficult, Tajik foreign minister Sirodjidin Mukhriddin admitted at the time.
The Islamic State (IS) group seized large swathes of Iraq in a lightning 2014 offensive, before the Iraqi government dislodged the jihadists from urban centres and eventually declared victory in December 2017.
The fall of the Islamic State's caliphate in Iraq and Syria has left many countries grappling with what to do with the jihadists and their relatives who want to return.
Tajik authorities have said over 1,000 citizens left the country to fight on the side of militant groups in Iraq and Syria after 2011, some after stints working abroad in Russia.
The most famous IS recruit from Tajikistan was Gulmurod Halimov, who headed the interior ministry's special forces unit before sensationally announcing his defection to IS in a video attributed to the group in 2015.
Source: DTN
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