A flare was aimed directly at the approach path of the aircraft as it came in to land at Barton airfield in Eccles, Greater Manchester, police said.
The aircrew said it appeared to come from the nearby campsite in Barton Moss Road at about 12.15am on Saturday.
But protesters countered that no flare had been fired from the camp and claimed Greater Manchester Police were using the incident as an excuse to search through their property.
Since November, campaigners have been at the drilling site in Barton Moss, between Barton Aerodrome and the M62.
Energy company IGas was granted permission for exploratory gas drilling and says it is seeking methane and shale gas but has no plans for fracking.
Police chiefs labelled Saturday's incident as an "unbelievably stupid act of criminality" that could have caused a "catastrophic situation".