He was accompanied by his lawyer Mr Nitithorn Lumlua.
Adm Prajun, however, rejected acknowledgement of the charges, and asked the TCSD investigators to revise the issuance of warrant for him to acknowledge the charges, pending the investigation of the Office of the Ombudsman.
He said after the Ombudsman finishes its finding, he is ready to come again to acknowledge the charges.
The Royal Thai Police charged him of defamation of the Royal Thai Police, and violation of the computer crime law after he was alleged to have posted a remark on the social media revealing that an unnamed army general had alleged of involvement in the trading of police positions.
Admiral Prajun said he called on Gen Prem last Friday to report him about the matter and he told the Privy Council chairman not to worry about his issue.
He asked Gen Prem to leave the job of fighting corruption with him as it is his duty to perform.
Gen Prem then blessed him good luck, Adm Prajun said.
Earlier Adm Prajun said he had no grudges whatsoever with Deputy Prime Minister Prawit Wongsuwan.
The admiral was also said to be a strong advocate to reform the police.
He had earlier said he would step down, over a case which former army chief and now deputy defence minister was alleged to get involved in irregularities in the controversial Rajabhakti museum park construction.
Gen Prawit dismissed allegations of position trading in the Royal Thai Police.