The three men, two aged 26 and a third aged 30, were arrested in the southern Dutch cities of Eindhoven and Arnhem, the prosecutor's office said in a statement.
"They are suspected of preparing terror attacks and wanting to join the Al-Nusra Front," Al-Qaeda's Syrian affiliate, it said, but did not give further details.
One of the men is also suspected of giving money to jihadist fighters in Syria.
Prosecutors started their probe during the summer after receiving information from the Dutch security services (AIVD), said the statement.
They also seized the men's passports as well as the passports of three other suspects.
Around 130 Dutch jihadists have left to fight in Syria, with 30 already having returned and 14 others killed in the fighting, according to the country's latest intelligence statistics.
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