Authorities are investigating radicalisation in the Dutch military.
The Dutch air force is currently operating in Jordan, taking part in an operation against IS in Iraq.
Sources say the sergeant was not involved in the mission, according to Netherlands` public broadcaster NOS.
The allegations are being investigated by the public prosecutor, the defence ministry said in a statement.
Defence Minister Jeanine Hennis Plasschaert said it would be "unpleasant" if it turned out that one man had "joined up with evil" while his colleagues "risked their lives for other people`s freedom".
Prime Minister Mark Rutte said the allegations were "extremely serious and painful", especially for the sergeant`s colleagues.
Officials have stressed that travelling overseas to join IS is a crime in the Netherlands.
The case would be the first time a serving member of the Dutch army has gone to Syria to join IS.
In January the country`s then Security Minister Ivo Opstelten said 180 Dutch jihadists were believed to have travelled to Iraq and Syria.
Several members of a Dutch motorcycle club, who were ex-servicemen, travelled to northern Iraq last year to help Kurdish forces fight against IS.
Dutch prosecutors told BBC News at the time that signing up with organisations like IS or the Kurdish militant group PKK was banned but joining a foreign armed force was no longer forbidden.
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