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Klaas Dijkhoff released the data in a letter amid an increasingly heated debate over immigration, stoked by an increase in arrivals from war zones across the Middle East.
He was responding to questions from members of parliament, many of whom have been calling on the government to start sending back migrants who are suspected of atrocities, or break Dutch laws.
Ten of the suspects were from Syria and the rest from Eritrea, Sudan, Nigeria, Georgia and other countries, he added, without going into further details.
Dutch news site AD reported that the Ministry of Security and Justice could not disclose what groups the suspects were part of while in Syria, so they could have been working either for the Assad regime or the opposition.
AD also wrote that it was not likely the suspects had been part of ISIS and that Dijkhoff had reported that so far, one person had been arrested for allegedly belonging to the terrorist group. The kinds of war crimes the Syrians are suspected of could not be disclosed either due to privacy concerns.
Dijkhoff said the Syrians could not be sent home because international treaties prohibit forced repatriation to a country where there is ongoing conflict.
A backlash against immigration has boosted the Netherlands' far-right anti-Islam Freedom party, whose leader Geert Wilders is regularly rated the country's most popular politician.