Addressing a press briefing Tuesday, Foreign Ministry spokesperson Tanju Bilgic termed the allegations in the UN Analytical Support and Sanctions Implementation Monitoring Team's report "baseless."
Bilgic said Turkey had designated both groups as "terrorist organizations" and the country was always part of international counter-terrorism groups in the struggle against ISIL. He also said that Turkey cooperated with the international community as well as the UN Analytic Support Group.
The UN monitoring team members visited Turkey in September, but during the visit they did not mention the allegation that Turkey was being used as a route to illegally smuggle weapons to ISIL.
The fight against the ISIL was discussed during the UN visit, but not these allegations, the spokesperson said.
"Everyone knows that ISIL has more military weapons, most of which were captured from Iraqi and Syrian armies. Especially, ISIL, which has gained a large part of Iraqi army’s ammunition and weapons in Mosul," he said.
"We requested clarification from the UN and expressed our reaction strongly," he added.
Iraq has been gripped by a security vacuum since June, when the ISIL stormed the northern province of Mosul and declared what it calls a caliphate in Iraq and Syria.
A U.S.-led international coalition is carrying out airstrikes to support Kurdish and central Iraqi government security forces in their fight against the group.