Speaking after talks with Croatian Prime Minister Ivo Sanader, Rehn said the arrest also showed that Croatia was determined to honour its international commitments.
He said the EU expected full cooperation with the UN war crimes tribunal in The Hague to continue, which Sanader promised.
Rehn went on to say that Croatia's EU entry negotiations, opened on October 3, had started well and that the first stage of the analysis of the adjustment of Croatian laws to European legal standards was proceeding well.
He voiced confidence concrete negotiations on individual chapters would begin early next year, and said the main challenges awaiting Croatia were reforms of the judiciary and state administration and the implementation of European legislation.
PM Sanader reiterated Croatia hoped to join the EU in 2009, which Rehn said was an ambitious plan, although he declined to speculate on dates.
Asked if during the negotiations the European Commission would support Italy's and Slovenia's demands of Zagreb, Rehn reiterated that bilateral issues, such as border disputes, were not within the Commission's jurisdiction. He said the Croatian-Slovene border dispute could be settled through international arbitration.
Rehn added that fisheries were within the jurisdiction of the Community and that the European Commission was a partner in such negotiations.