The Apache helicopter made a forced landing during a military exercise, the UN force in Mali said in a statement.
The Dutch armed forces chief, Gen Tom Middendorp, said: “Everything points to this being an accident.”
The aircraft was from the Minusma mission charged with peacekeeping since Islamist fighters were forced out.
One crew member survived the crash but died later of his injuries at a French field hospital, Gen Middendorp told a news conference in The Hague.
Gen Middendorp said an investigation into the cause of the crash was under way.
“The Netherlands is profoundly touched by this terrible accident,” Prime Minister Mark Rutte said.
The Netherlands has 450 military personnel in Mali as part of the 11,000-strong UN mission.
Minusma took over security duties from France in 2013 after France had intervened to stop an Islamist insurgency a year earlier.
The mission has suffered regular attacks from militants. Earlier this month, a rocket attack on a UN base in northern Mali killed three people.