Mesic and Sanader commented on the transfer of Croatian troops within the ISAF mission to Kandahar, a war zone and one of the biggest Taliban strongholds in south Afghanistan, after a special parliament session on the occasion of Independence Day.
Sanader said he expected a report on the matter from the foreign and defence ministries.
He recalled that Croatia was in Afghanistan as part of an international mission which was not subject to national command.
"As prime minister, I want to know what this is about," Sanader said.
Asked by the press if he would be willing to initiate the withdrawal of Croatian troops from Afghanistan if it transpired that their engagement was contrary to Croatian parliamentary decisions, Sanader said he would wait for the report and then inform the public.
Mesic said he had been informed about the transfer of Croatian troops and added that their task in the crisis area of south Afghanistan would not be to fight but act solely as instructors.
"It is one thing to be an instructor and another to fight," said Mesic.