Mr Gaynor, an Army Reserve Intelligence Officer, has posted a series of blogs arguing Islam immigration should be limited and in the wake of the Boston bombings re-aired his views.
He said he was charged on Monday by the ADF for bringing the organisation into disrepute and responded by saying it was proof political correctness was hampering the ADF's ability to fight against Islamic violence.
"It is outrageous that the Australian Defence Force is charging me for discussing Islam," he said in a statement.
"In the last week, ASIO has confirmed hundreds of Muslim Australians are joining violent Islamic groups in Syria and a radical Australian Islamic cleric has been linked to the Boston bombers.
"Yet the Australian Defence Force is sending a message that intelligence officers cannot discuss Islam in any way, shape or form, unless they pass judgment that it is a nice, peaceful religion.