They also discussed Croatia's efforts to join the European Union and the current crisis in the Union caused by the referendums in France and the Netherlands which rejected the EU Constitution.
Sanader voiced gratitude for the support which Bavaria had been offering Croatia from its independence.
"We expect positive headway and the start of the talks with the EU in the near future and we know that we enjoy the German and Bavarian support for this start," Sanader told reporters after his talks with Stoiber.
"We are sure that both the EU and Croatia will profit together from Croatia's entry (into the EU), when all conditions are met and the negotiations completed. We are ready for the negotiations, we have a negotiating team in Croatia. The European Commission has adopted a negotiating framework and only the green light for the start of the negotiations is being awaited," the Croatian premier said.
Stoiber said that the EU was currently in a very grave crisis and that the French and Dutch 'No' at the referendums were only the reflection of that crisis, which he added was partly caused by the admission of new members. The crisis is temporary and will be solved, the Bavarian Minister President said. According to him, the crisis regarding the EU enlargement was partly caused by plans of the European bloc to start entry talks with Turkey.
Commenting on the EU and the remaining condition for opening the entry talks with Croatia, namely its full cooperation with the UN war crimes tribunal, the Croatian premier recalled that his cabinet's Action Plan aimed at locating the runaway general Ante Gotovina was assessed as good, as was its implementation.
He added that Croatia expected "the letter which the (tribunal's chief prosecutor Carla) Del Ponte is sending today to Luxembourg and its Foreign Minister Jean Asselborn to state so".
Stoiber said that good political relations between Bavaria and Croatia were being advanced with economic cooperation. Trade between Bavaria and Croatia now totals over half a billion euros.
Sanader said that Bavaria was one the biggest investors in Croatia. The Bavarian-Croatian joint commission has existed for more than 30 years, he stressed.