"With negotiations underway, there can be no doubt about our joint objective: full EU membership for Croatia," Barroso said in his 15-minute address, which was attended by top Croatian officials and foreign diplomats accredited to Zagreb.
"How things progress from here is in your hands. Negotiations will proceed on the basis of Croatia's own merits and its ability to meet all the requirements for membership," he said.
"I appreciate your ambition to make rapid progress in the negotiations. But if you are to succeed, you should not underestimate the extent of the work that needs to be undertaken."
Barroso said that the Croatian Parliament would be playing a crucial role in the accession process, and added that the Commission's experience had shown how important it was that candidate countries enjoyed full cross-party participation and a national consensus on European integration issues.
The European Commission president also stressed the importance of engaging all citizens in an open debate on EU membership-related issues, providing adequate information and avoiding unrealistic expectations.
"The membership conditions are well known," Barroso said, citing the necessary progress on what are known as the Copenhagen political and economic criteria, and the need to meet the commitments from the Stabilisation and Association Agreement, including full cooperation with the Hague war crimes tribunal and making progress on regional cooperation.
Commenting on negative reactions in Croatia to the idea of a regional free trade zone, Barroso said: "The EU's own experience shows that regional trade integration brings great benefits. It can benefit Croatia too, by attracting investment, providing access to wider markets for Croatian goods and increasing stability in the region. It is not a substitute for accession, it is fundamental part of European integration."
Barroso also spoke of citizens' fears about some negotiating chapters, such as one concerning the sale of real estate to foreign nationals.
"There are a number of other issues and chapters of the negotiations which will pose particular challenges, and I am sure that we will see a real commitment to solve them. But nobody said negotiations for accession would be easy. It is a process which all acceding member states, including my own, have had to go through," he said.
"Only with constant, intensive work by the Croatian authorities on legislative alignment, the building up of administrative capacity and correct enforcement, will the negotiations be able to proceed at a good pace. And the first step is to ensure the adoption of quality legislation," he added.
Barroso also said that Croatia should not neglect the key outstanding issues under the political criteria, such as the rights of minorities, refugee return, impartial prosecution of war crimes trials, media freedom, judicial and public administration reform, and fighting corruption.
"The progress you make in these areas will make Croatia a leading example for the whole region," Barroso said.
On the subject of the economy, the EC president said that Croatia needed to consolidate its market economy status, prepare itself to cope with the competitive pressures of the EU and attract more foreign investment.
"But Croatia has already achieved a lot," Barroso said, noting that its macroeconomic policy had contributed to relatively low inflation and a stable exchange rate and significantly reduced budget and current account deficits.