Mr Pongniwat stressed that public prosecutors should remain an independent organisation to ensure impartiality.
He said he was opposed to a proposal that the prosecution should be "returned" to the Justice Ministry.
If this happens, prosecutors would be under the supervision of the executive branch.
Asked about the possible extradition of former prime minister Thaksin Shinawatra, he said prosecutors have been working on it but he noted that the extradition process involves several agencies, including the Foreign Ministry and the Royal Thai Police.