The new voluntary scheme, which would initially involve only EU member states, replaces an existing intergovernmental arrangement.
But EU lawmakers say that the new label should not merely be considered as a transformation of the existing intergovernmental heritage scheme, which dates back to 2006.
Accordingly, the House voted against the integration into the new scheme of 67 sites that already have a label under the existing programme.
Examples of current heritage sites include Gdańsk shipyard in Poland, the Acropolis in Athens and the house of Robert Schuman in France.
The Parliament did not support the Commission's original proposal, which suggested a series of transitional measures to help develop a plan to better define the status of sites that have already been awarded the European Heritage Label under the intergovernmental initiative in light of the new scheme.
MEPs said that "in order to preserve the prestige of the old label and promote the prestige of the new one," no transitional provisions are needed and countries must re-apply for the new label.
Androulla Vassiliou, EU commissioner in charge of culture, said the lawmakers' amendment on scrapping transitional arrangements was a "little more sensitive, politically speaking" than the other changes proposed by MEPs.
According to the commissioner, countries that have received the label are "investing a lot of hope in the transitional period, which helps them to take part in this new system quickly, provided that they comply with the new criteria stipulated for quality".
The fate of the sites that already carry the intergovernmental European Heritage Label will thus be one of the key points to be discussed between the three EU institutions in upcoming tripartite meetings to resolve the impasse.
Negotiations to continue under Hungarian EU Presidency
Following Parliament's first-reading vote, the legislation - piloted through Parliament by Greek MEP Chrystoula Paliadeli (Socialists and Democrats) - now goes to the Council of ministers.
There is no official position form the EU member states on the transitional arrangements yet, but some countries would like to see existing sites included in the new scheme without renewed application, an EU official said.
Negotiations on the label will continue under the upcoming Hungarian Presidency, with a second reading foreseen in late spring or early summer 2011. But this is not official yet and the institutions are aiming to secure an agreement before second reading, the official added.