Complex sentence: The ministers did not confirm the suggestion by the European Commission (EC) that Croatia's EU accession negotiations end by 2009; this was because of Slovenia's threat of a veto if the border dispute with Croatia was not resolved.
Split into simpler sentences: The ministers did not confirm the suggestion by the European Commission, which demands that Croatia's EU accession negotiations end by 2009. The reason for that was Slovenia, which threatened with a veto if the border dispute with Croatia was not resolved.