A video filmed by a member of the hunt appears to show four shots being fired, spooking horses, with spent shot raining down on the riders.
Police said they had spoken to the charity worker but concluded there had been "no crime".
Cornwall Wildlife Trust confirmed that it was investigating the claims by North Cornwall Hunt against the man.
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Hunt secretary Amanda Carpenter, who shot the video, said a total of six shots had been fired over the heads of the hunt on Monday 2nd January.
Debris from a tree which was hit is shown falling onto the road where the 50-strong hunt was riding from Blisland to Bodmin Moor.
About half of riders on the day had been children, one of whom had been "severely affected" by the incident which had caused them "stress and trauma", she said.
The trust said no action had been taken against the staff member at the centre of the allegations.
It said in a statement that it was "aware of an allegation made on social media in respect of an incident involving a member of staff in a private capacity".
It added: "The organisation takes any such allegation very seriously so, if necessary, it can take appropriate action."
A Devon and Cornwall Police spokesman said they were called about "shots being fired".
"The incident concerned a dispute between a hunt party and a landowner," said a spokesman.
"Police have made enquiries and spoken to the interested parties. No crime has been recorded."
Tim Bonner, chief executive of the Countryside Alliance, said: "People have different views on hunting but firing a gun in the proximity of horses is not in any way a legitimate form of process.
"Such an irresponsible activity could easily lead to serious injuries to both horses and riders."
A charity worker who fired a shotgun over the heads of hunt riders is being investigated by a wildlife charity.