Marcos maintained the ICC has no jurisdiction over the Southeast Asian country, which withdrew from the ICC in March 2019.
"We will not cooperate with them in any way, shape or form," Marcos told reporters, just days after appeals judges at the ICC rejected the Philippines' attempt to block an investigation by the court's prosecutors into the anti-narcotics campaign of former president Rodrigo Duterte.
Thousands of people were killed during anti-drug operations that ended in shootouts during Duterte's six-year term, rights groups say. Police have officially acknowledged roughly 6,200 deaths and reject accusations of systematic executions and cover-ups.
Marcos said the alleged crimes must be dealt with in the country as they were committed in Philippine territory. The justice ministry has promised its own investigation into the drugs war will be fair.
"We continue to defend the sovereignty of the Philippines and continue to question the jurisdiction of the ICC in their investigations here in the Philippines," Marcos said.
While the Philippines is no longer a signatory to the international tribunal, the ICC's top prosecutor has said the court does have jurisdiction because the country was a party at the time the alleged crimes were committed.