Prosecutors have now launched a criminal investigation into the 26-year-old air force sergeant, who has not been identified.
The man has been suspended from duty, and his access to all defence information revoked. It was not immediately known where he was serving and what classified military information he may have been privy to.
"It goes without saying that travelling abroad and joining ISIS is unacceptable, and is also a criminal offence," Defence Minister Jeanine Hennis Plasschaert said in a statement.
Read: Spain, Morocco arrest 14 suspected of recruiting for Islamic State
It is the first time that a Dutch soldier on active duty has deserted to join the forces of the Islamic State militant group, which has captured a large swathe of Iraq and Syria since early 2014.
There have been cases in the past of former Dutch soldiers travelling to join the IS group.
Around 180 Dutch nationals have journeyed to join IS or other Islamist groups, according to the figures published by the Dutch security service AIVD in April. Around 20 have been killed in fighting, and 35 have returned to the Netherlands.
A report by the service said there were believed to be "several hundred" militants in the Netherlands, and "thousands" of sympathisers.
Read: UK officials charge two men with trying to join Islamic State
"Every case of radicalisation is one too many," said Plasschaert Thursday, adding it was "disappointing" that an active soldier had run away to join the militants "while their colleagues are risking their lives for the freedom of others."
The Netherlands has joined a US-led international coalition fighting IS, and has taken part in air strikes on the group in Iraq. It has also sent six F-16s to take part in the air campaign, and deployed Dutch military trainers to help the Iraqi forces.
Dutch soldiers from its royal air force are currently station in Jordan, but the missing sergeant is believed to have left from the Netherlands for Syria, Dutch media said.
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