He held this post until he was nominated Commissioner for Fisheries and Maritime Affairs in 2004, upon Malta's accession to the EU.

[2] As European Commissioner, he has been responsible for spearheading the EU's Integrated Maritime Policy and for innovative measures in fisheries, particularly through the involvement of stakeholders and the fight against illegal fishing activities, aimed at achieving sustainability in the sector.

Borg courted controversy among environmental groups by fiercely opposing the ban on the sale of Bluefin tuna, an increasingly rare fish which sells for thousands of pounds in Japan.

His position on Bluefin tuna has been linked to the fact that the industry earns €100 million annually for Malta.

[4] Soon after the end of his term as Fisheries Commissioner in 2010, he was appointed chairman of the Mediterranean Academy of Diplomatic Studies[1] and resumed lecturing at the University of Malta.