Nasser Yeehma received the certificate and a badge from Air Marshal Vorachat Tharechat, commander of RTAF Security Forces Command.
Mr Nasser serves as chief guard for the Network of Students and People for the Reform of Thailand (NSPRT), known for taking a more hardline anti-government stance than some other groups.
The RTAF on Saturday issued a clarification after Mr Nasser posted a picture on his Facebook page of himself holding the certificate, along with a message saying that it had been awarded in recognition of his "fight for the country".
The message also said: "I insist that for this award [of certificate], the RTAF does not look at 'intention' only."
The certificate has Mr Nasser's name and is signed by AM Vorachat. The picture went viral and raised speculations about connections between the air force and Mr Nasser and NSPRT political activities.
Air force spokesman AM Monthon Sutchukorn explained that the certificate and the wing badge in question were given to recognise people who had made contributions or provided support to work of the agency or the air force.
Anyone with the proper qualifications could file a request with the Security Forces Command's parachute department and pay 700 baht to receive the certificate and the emblem without having to take part in real parachute traning, he added.
The applicants were from both the private and public sectors and usually their requests were combined into a single file. The air force, however, would look into Mr Nasser’s case since it had received media and public attention, AM Monthon said, adding that authorities had recorded the names of all certificate recipients.
AM Monthon confirmed that Mr Nasser's receipt of the award was not related to politics. He said the air force regularly received the requests and the certificates had been issued to qualified people for years.