"Two incidents in which there may have been possible civilian casualties are being investigated in around 1,300 missions carried out by the Netherlands," The Hague-based government said in a letter to parliament late yesterday.
Citing "operational reasons", the Defence Ministry said neither details of the incidents nor the probe are being made public.
The probe was prompted by a raft of questions raised by lawmakers in parliament on the Netherlands' role in the fight against IS after The Hague announced last month it would expand air operations into Syria.
"The incidents are being investigated by the Defence Ministry and details will be passed to the Public Prosecutor's Office," said the letter, posted on the Defence Ministry's website.
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"Because of several reasons it's impossible to determine the regrettable number civilian deaths as a result of coalition operations," it added.
The Netherlands is participating in the Iraq strikes with four F-16 aircraft specialising in close air support of ground operations by Iraqi forces.
Dutch Prime Minister Mark Rutte said the extended air operations will now target eastern Syria "in particular to stop the IS 'pipeline' leading from Syria into Iraq."
US air strikes in Iraq began in August 2014 after IS captured a swathe of territory in Iraq and Syria in a lightning offensive.
Washington and Arab allies broadened the strikes against IS in Syria a month later in September 2014, with the US also leading moves to build an international coalition of some 60 nations against the jihadists.