"So far the tribunal has not been able to say there was full cooperation," Barroso said after talks with Croatian President Stjepan Mesic in Brussels on Tuesday.
Barroso could not forecast what kind of decision the European Council would make regarding the start of entry talks with Croatia.
'We are expecting a new report by the tribunal's chief prosecutor Carla del Ponte in early March which will serve as a basis for the Council's decision," Barroso told reporters.
President Mesic said that in his opinion Croatia was cooperating with the Hague tribunal given that it had met 625 out of 626 requests presented by the Tribunal.
"We have not handed over General Gotovina because he is beyond reach of the Croatian authorities. We should arrest and transfer him or find out his movements, in which we need assistance from other countries," Mesic said.
Barroso said that he fully believed in the good will of President Mesic, adding that this, however, did not mean that "all the structures in the state are really giving full cooperation".
We must be confident in the full cooperation of the country. According to the tribunal's opinion, this has not been the case so far. I hope that by 17 March there will be new elements that will assure us of the full cooperation, the European Commission chief said.
Mesic said that on Wednesday he, Prime Minister Ivo Sanader and Sabor Speaker Vladimir Seks would send a letter to the EU, NATO and the Hague-based tribunal with comprehensive documentation of Zagreb's efforts to find the general.
"In the letter we will indicate possible movements of Gotovina since we know that he is not in Croatia," Mesic said.
Earlier in the day, Mesic had lunch with King Albert II of Belgium and then held talks with NATO Secretary General Jaap de Hoop Scheffer.
On Wednesday, Mesic is due to meet Belgian Prime Minister Guy Verhofstadt, European Parliament President Josep Borrell Fontelles, and the EU High Commissioner for the Common Foreign and Security Policy, Javier Solana.