This is in relation to Mr Vele's alleged involvement in the release of funds to an Israeli company for the purchase of two generator sets in 2014.
Former Opposition Leader Belden Namah had initially lodged a complaint with the National Fraud and Anti-Corruption Directorate against Prime Minister Peter O'Neill for allegedly directing Mr Vele to make the payment.
Commissioner Baki confirmed the District Court issued a warrant of arrest for Mr Vele last Wednesday which by law, should be executed.
"On Sunday 26th I directed that the District Court order obtained be executed immediately and have Secretary Vele brought before the court to answer to his charges."
However Mr Baki says he's disappointed because he was never briefed on the matter until Saturday after it was made public on social media.
Meanwhile the National Fraud and Anti-Corruption Directorate will come under internal police investigations into its operations of past, current and pending investigations.
Commissioner Gari Baki says the Acting Deputy Commissioner Raphael Huafolo will lead the investigation team.
He says there's a strong perception that the directorate is heavily politicized and is not impartial in all matters being investigated.
The directorate is headed by Chief Superintendent Mathew Damaru and his assistant Chief Inspector Timothy Gitua.
"The actions of Damaru and Gitua undermines the integrity of the Office of the Commissioner. This is a serious breach of discipline and it amounts to insubordination. In fact they are treating the Office of the Commissioner with contempt. Why wasn't I briefed prior to the securing of the arrest warrant? Why wasn't I briefed three days prior to my directive for the briefing, having read this in the Facebook." NBC/ONE PNG