North Wales Police said the pilots were being treated for minor injuries following the incident in the Pencarnisiog area of Anglesey.
The force said helicopters from the Coastguard and the Wales Air Ambulance were at the scene close to RAF Valley on the island.
"Two pilots are being treated for what are thought to be minor injuries and at this stage there are no reports of any wider damage or injuries," it said.
"Please avoid the area until further notice."
The Ministry of Defence has been asked to comment.
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