Despite the efforts made by Croatia so far, full cooperation with The Hague means that this last step must also be taken, Scheffer told reporters after meeting Croatian President Stjepan Mesic in Brussels.
Mesic said there was no doubt that Gotovina would be arrested if he was in Croatia, but added that if he was not Croatia would need assistance from other countries in its efforts to locate him.
"Figuratively speaking, if Gotovina were in Paraguay, we obviously would not be able to extradite him. If we find out that he is in Croatia, he will be arrested and extradited to The Hague," Mesic said.
Mesic said that there used to be elements within Croatian authorities that protected fugitives from the Hague tribunal, but that there were no more of them.
Mesic confirmed that he, Parliament President Vladimir Seks and Prime Minister Ivo Sanader had written a joint letter on Monday providing evidence of Croatia's cooperation with the Hague tribunal, and that the letter contained "hundreds of pieces of evidence of what Croatia has done".
The letter will be sent to all members of the European Union and NATO and to all European institutions.
The NATO secretary general praised Croatia's progress in adjusting its armed forces to NATO standards, but pointed out that the country was yet to achieve the goal of allocating two per cent of Gross Domestic Product for the military.
He thanked Croatia for its contribution to the NATO peacekeeping mission in Afghanistan, and said that its contribution to other Alliance operations, such as training of Iraqi soldiers, would be welcome.
If Croatia will be in a position to participate, it will be welcome. That is up to the Croatian government, Scheffer said.
On the first day of his two-day visit to Brussels, Mesic had lunch with King Albert II of Belgium. Later in the day he was scheduled to meet European Commission President Jose Manuel Barroso.