The European Commission will not ignore Malta's objections to the new Frontex rules and wants to step up dialogue to resolve the matter, according to Home Affairs Commissioner Cecilia Malmström.
Reacting to Malta's decision not to take part in future Frontex missions under these guidelines, Ms Malmström said the EU executive was still committed to ensuring the island's cooperation in these patrols.
"I read the reactions in the media and, of course, there will be further discussions. This is important as Malta is an island in the middle of the Mediterranean and now that the illegal immigration 'season' is starting it's important to cooperate," Ms Malmström said.
However, she stressed that during the discussions on the guidelines Malta "went along with the proposals".
She said: "Malta was present when the discussions were held and they abstained. But at the end of the day (Malta) still went along with the proposals and we will continue with the discussions with them now."
According to the controversial guidelines, intended for use in future anti-migration missions, the member state hosting the mission will have to take in all the immigrants rescued on the high seas, as opposed to the closest safe port of call.
The Prime Minister has insisted that Malta will not take part in Frontex missions under these rules. He also suggested that a different arrangement could be reached among the countries which take part in the mission, in which case there would be no problem for the island to take part.
When originally proposed, the guidelines were obligatory but following Malta's insistence they were changed to "non-binding", meaning the rules could be ignored if member states joining a Frontex mission agreed on some sort of different code of engagement.
Asked why Malta decided to abstain instead of completely turning down the guidelines by voting against, a government spokesman said this was done after Malta's non-binding proposal was taken on board.
Although at the end of the day, abstaining or voting against would have made no difference as the majority of member states were in favour, observers think a resounding "no" by Malta would have sent a stronger political message.
According to the government spokesman, Malta still made its position against the rules "very clear" in a declaration made during the Council meeting.
The text of this declaration says: "Nothing in this proposed Council decision should be considered as modifying the Convention of Safety of Life at Sea (Solas) and the Search and Rescue Convention (SAR) as they apply to Malta."
It adds: "Malta's obligation at international law is to disembark rescued persons at the geographically closest place of safety and Malta rejects all attempts to erode this position."
Nationalist MEP Simon Busuttil moved a resolution to reject the new rules but this failed to garner the needed two thirds majority in the European Parliament last week, being outdone by 33 votes.
After the vote, Dr Busuttil accused his Labour counterparts of failing Malta's national interests when they did not manage to convince their political group to support this resolution. But Labour retaliated, pointing out that the government had failed to convince other member states to block the proposals at Council level and even abstained during the vote.
MEPs David Casa, Louis Grech and Edward Scicluna, along with Dr Busuttil, voted against the guidelines' introduction, while Labour MEP John Attard Montalto was absent.
Mr Grech, Labour's head of delegation in Brussels, and Dr Attard Montalto have so far failed to explain the latter's absence from this vote.