A new EU law that reforms the bloc's migration and asylum systems will add to Malta's burden in some instances, Home Affairs Minister Byron Camilleri said on Wednesday.
The law is no "magic wand" and those who are painting it as a solution to the migration problem will have to answer to EU citizens in a few months "when the reality is different", he wrote in a Facebook post.
"The pact strengthens solidarity between countries but in other instances will add even more burden to border countries like Malta," he said
"Therefore, neither does it strike a balance between responsibility and solidarity, nor does it give border countries peace of mind that their needs will be fully addressed."
Malta is the only EU border country so far to express concerns over the deal. Italy, Spain and Greece welcomed it earlier on Wednesday.
Meanwhile, Hungary rejected it.
Agreement reached on Wednesday
EU lawmakers reached the agreement on Wednesday. It will overhaul the bloc's laws on handling asylum-seekers and migrants.
The reform includes speedier vetting of irregular arrivals, creating border detention centres, accelerated deportation for rejected asylum applicants and a solidarity mechanism to take pressure off southern countries experiencing big inflows.
European Parliament president Roberta Metsola hailed the deal in a press conference on Wednesday morning.
This was maybe "the most important legislative deal of the mandate", she said, and promised the 'historic' package would make a difference.
But an entire spectrum of local and international migrant NGOs lambasted the deal, saying it was more like a 'historic failure'.
More migrants will die because of the pact, and the ones that reach Europe's shores will have an even harder time. The pact was a bow to Europe's right-wing parties, they said.
'No magic wand'
Minister Camilleri said the deal was an attempt at a compromise between countries that have long been suffering from the problem and others who have no interest in helping in any tangible way, primarily through relocating asylum seekers that arrive in border countries like Malta.
The pact is no "magic wand", he said. The problem will not be mitigated and will not cease to exist.
"Those who are painting this agreement as a solution to migration will have to answer to Maltese and Europeans in a few months when reality will be different."
He also said Malta was proactive, taking action before the EU agreement was even reached, and this year alone had relocated a record number of failed asylum seekers to their countries of origin.
The central Mediterranean crossing, between North Africa and Italy and Malta, is the world's deadliest migration route, with more than 2,200 deaths this year alone, according to the UN.