Malta is protesting after being shortchanged by the EU over funds for energy and broadband related projects.
Malta and Cyprus have been allocated just €20 million from a €5 billion pot of unspent EU funds.
The Sunday Times has learnt that high ranking Commission officials had originally promised much more, prompting one official to describe the sum as a "pittance".
Sources said Malta was very surprised at the final decision as it was clear that "someone didn't keep his word".
Malta had lobbied hard for these funds, with Prime Minister Lawrence Gonzi holding meetings with the Czech Prime Minister, who currently holds the EU Presidency, and the European Commission President last December.
It is estimated that Malta's two main energy-related projects require an investment of about €200 million.
The day after the Commission's proposal was announced, Malta's Permanent Representative in Brussels Richard Cachia Caruana objected to the manner in which the Commission decided to distribute these funds.
Malta is again expected to voice its objections on Tuesday, when EU Finance Ministers gather in Brussels to discuss the issue.
The decision to distribute these €5 billion EU funds comes amid increasing opposition from various member states, including Malta, as well as legal concerns raised this week by the European Commission's internal legal services.
Malta has various projects in the pipeline, including the construction of its first wind farm and the laying of an interconnection cable to connect the island with the European energy grid.
Mr Cachia Caruana told fellow EU ambassadors during their weekly meeting that in Malta's opinion, the Commission's proposal did not adequately reflect the essential elements of decisions taken by EU leaders last December on the need to strengthen trans-European energy networks with particular attention to be given to interconnections and the connection of the most isolated European countries.
He said that Malta found it unacceptable that with all these funds at its disposal, the Commission was unable to specifically include mature projects which would have linked the maximum possible number of isolated member states to the European energy grid.
Italy and many of the new member states are also objecting to the Commission's proposals.
According to EU sources, the German government is reluctant to see money that would normally be returned to government coffers being spent on common projects.
In a new twist last week, it was revealed that the Commission's own legal services had judged that most of the money allocated may not be used in the way proposed by the EU executive, as this went against the provisions of the EU Treaty.
However, a Commission spokes-man said that although it was aware of this position, the Commission was determined to forge ahead .
EU sources said that although opposition from member states to the Commission's proposals was increasing, this did not necessarily mean that the proposal would be amended.
"This is a very difficult task for the Commission because although €5 billion of funds might seem a lot, it is far from enough to please everyone. In this scenario it is very difficult (for there to be) a revision - and that Malta gets additional funds," the sources said.