"This proposal was not put forward by the Croatian EU presidency, a Croatian ministry or the Croatian government. This point is again being raised by the European Commission during our presidency and is yet to be discussed," Butkovic told the press before an inner cabinet meeting.
"Croatia's position on the matter is logical and normal. We will not be asking for air companies to get richer at the expense of end users, that is citizens," the minister added.
Under EU rules, travellers are entitled to up to €600 compensation if a flight is delayed by at least three hours or cancelled less than 14 days before departure. They can also receive compensation if they are denied boarding.
Some national authorities and courts have criticised the rules, saying member states struggle to process the large number of claims they receive, and airlines' compensation payments have grown because the number of delays and cancellations has risen.
Talks among EU governments on revising passengers' rights, which have been in place since 2005, are due to start in the coming weeks. Any agreement will be considered by the European Commission and Parliament.
The European Commission proposed in 2013 that the minimum flight delay be increased from three to five hours, but negotiations stalled after that.
An informal document circulated among member states has proposed keeping the level of compensation the same as now for passengers, but suggested increasing the minimum flight delay for which airlines must make payments.
In 2018, 17.6 million passengers were affected by flight cancellations and 16.5 million by long delays.