The helicopter, from the UN's MINUSMA mission, crashed about 20 kilometres (12 miles) from Gao, a source from the city's airport told AFP, adding that two people were injured and subsequently died.
Top Dutch defence commander, General Tom Middendorp later confirmed the crash at a press conference in The Hague.
"This afternoon around 1300 GMT a Dutch Apache attack helicopter crashed in Mali," Middendorp said.
"A 30-year-old captain and 26-year-old first lieutenant died in the accident."
Middendorp said Dutch investigators were probing the crash.
Also Read
Both men were members of 301 Squadron based in Gilze-Rijen airbase in southern Netherlands.
MINUSMA has some 11,000 personnel on the ground in Mali, around 670 of whom come from the Netherlands.
With more than 40 peacekeepers killed since its inception in 2013, MINUSMA is considered the most dangerous UN mission in the world, particularly for the Chadian contingent, which has sustained a large proportion of the casualties.