"We wish to know why our territory is used, if it is used," he told Reuters in San Francisco.
"A part of my constitutional powers is also the appointment of the heads of the intelligence services, so the government and myself have information about the work of the intelligence services," Mesic said. "We have not received any information."
AI Croatia asked the Croatian government last week to urgently investigate claims from an AI report alleging that a plane which CIA had used to transport terror suspects had used Dobrovnik's Cilipi airport as a transfer point.
AI said on its web pages on Wednesday that a Boeing 737, which international humanitarian organisations claim CIA used to transfer terror suspects between 2002 and 2005, landed at Cilipi twice.
Mesic, who arrived in San Francisco on Saturday after a visit to South Korea, said it would be possible for an aircraft to "deceive" airport authorities about the passenger manifest.
"If any aircraft stops over for reasons that are not known to me such as technical reasons and stays for a while at an airport, we cannot know who the passengers are, or where they
are bound for," he said.