In a television interview, Wycoco admitted he has yet to receive a copy of the one-page Department of Justice (DOJ) order.
"I will seek further clarification. We will ask for additional guidelines because if we ban arrests at night baka dumami ang kriminal. Ang mga kriminal di naman natutulog yan," he said.
The NBI is the investigation arm of the DOJ.
"Of course, he is our boss (Secretary Gonzalez). We will comply with his instructions. However, we stress that it has been the policy of the NBI to refrain from conducting night arrests, particularly on Friday nights and weekends," he said in a statement.
The ban on night operations is intended to diminish complaints of human right violations against NBI operatives.
The DOJ instructed the NBI to cease and desist from arresting and/or inviting suspects during the nighttime operations unless they are fugitives from justice; escaped prisoners; and are targets in accordance with the rules of "hot pursuits."
"Operations are allowed when there is strong evidence that a crime has been committed or is about to be committed and the crime is serious and there are strong reasons to believe that the suspect or suspects must be neutralized in order to maintain the peace and order in the community especially crimes against natural security," the order stated.
Wycoco believes the DOJ only had the best interest of the NBI when it issued the order, but clarified that the bureau has never been a violator of human rights.
"As much as possible, the NBI does not make apprehensions during Fridays and weekends because there are no prosecutors on duty full-time. They will only conduct special operations if there is a risk of flight or the suspect is a dangerous criminal or involved in a heinous crime," he said.
The order stemmed from an alleged warrantless arrest made by NBI agents against a couple, including the daughter of a congressman from a northern province. They were detained for allegedly traveling on board motorcycles without documents in Taguig City.
The NBI explained that elements of the NBI Anti-Fraud and Computer Crimes (AFCC) unit conducted the operation last March 1.
They received information that motorcycles with falsified registration documents were seen in the area.
They invited six owners of big bikes, all members of the Disciples Motorcycle Club, to their office for questioning. They were released after promising to present the proper documents the following day.