The attack happened in the Rumangabo region of North Kivu province, where M23 has been battling government forces and UN peacekeepers for 18 months. No casualties were reported.
MONUSCO chief Martin Kobler condemned the attack and said "M23 rebels will not prevent us from using the Congolese air space. We shall continue doing all in our power to defend civilian populations including by using force if necessary."
An M23 spokesman, Vianney Kazarama, told AFP in DR Congo that rebel fighters thought the helicopter was carrying government and UN forces to launch an attack.
"So they opened fire with machine guns," he said. The rebel spokesman speculated that the UN pilot may have drifted from a normal route and gone too close to an M23 camp at Rumangabo.
M23 launched a mutiny against the DR Congo government in North Kivu in early 2012 and for a while seized the major eastern city of Goma. The UN has sent an offensive intervention brigade to the region to battle M23 and other armed groups, forcing the rebels away from Goma.
The UN is to start using surveillance drones for the first time in eastern DR Congo in November, MONUSCO said earlier.
The drones will monitor rebel movements and the border with Rwanda. UN experts have accused Rwanda of aiding M23. Rwanda strongly denies the charge.