Customs Deputy Commissioner Celso Templo, Intelligence and Enforcement Group chief, said the investigation would also focus on documents and statements issued by both camps.
Templo said the panel would coordinate with the National Bureau of Investigation and the Criminal Investigation and Detection Group to validate the accusation of Marcos.
"We are leaving it to the panel," he said. "We want to come up with an independent result."
Marcos has accused Morales of "protecting" three big-time smugglers whom she identified only as "DT," "BS" and "BT."
She challenged Morales to come up with a list of smugglers and bring them to court to prove that he is serious in his campaign against smuggling.
Marcos said because of continuous smuggling, the government is losing an estimated P32 million in daily Customs duties, which average P80,000 per container.
"I don’t understand why despite the dozens of law enforcement agencies and anti-smuggling task forces assigned to go after smugglers, not one big-time smuggler has been jailed or has been formally charged in court," she said.
Marcos said the three alleged smugglers belong to a group of importers and brokers who control over 400 containers a day. They bring in European luxury cars, fighting cocks, electronic items, garments, food items, tiles, sugar and other highly dutiable goods through a "Super Green Lane" manned by "friendly Customs personnel," she added.