"Political agreement was reached by a qualified majority on urgent measures for the fishing sector," the presidency said, as the ministers met into the evening in Brussels.
The European Commission says that fuel prices for fishing boats have soared 240 percent since 2002, putting severe pressure on a sector already struggling to cope with overcapacity and dwindling fish stocks.
Fishermen have led waves of often militant protests mainly across southern Europe in recent months against the rising cost of fuel, including in Brussels where one incident caused minor damage to an EU building.
The emergency package will be spread over several years, with 1.4 billion euros coming from the European Fisheries Fund, which has a budget of 4.3 billion euros for the period from 2007 to 2013.
Under the agreement, the money can now be used in a more flexible manner.
The remainder, 600 million euros, will be covered by the commission, under a plan it announced a week ago.
While the emergency package was given the green light, not all nations agreed and a vote was called. Three countries -- Austria, Denmark and Sweden -- opposed it, an EU diplomat said.
The European Union's executive arm said that the funds were aimed in part at encouraging the restructuring of segments of fishing fleets hardest hit by the fuel crisis.
The new money only became available after European Commission President Jose Manuel Barroso leaned on his staff in the face of reluctance from some commissioners to lift subsidies.
However, after fuel prices protests, he was encouraged by countries such as France, whose fishing sector has long complained that its cries for help fall on deaf ears in Brussels.
The package would lift the amount of public aid allowed in the sector from the current 30,000 euros per operation over three years to 100,000 euros, as urged by France and Italy.
The commission also pledged to consider emergency aid to help fishermen who abstain from going out to sea during a maximum period of three months, as long as it is part of a restructuring.
The EU executive also plans to allow early retirement aid on a broader basis.
The package also foresees aid for investments in equipment such as boat motors that are more fuel efficient and helping fishermen earn more for what they catch.
"High fuel prices and chronic overcapacity mean that European fisheries are in a time of crisis," EU Fisheries Commissioner Joe Borg said on July 8. "The commission recognises the need to help the sector adjust to the new realities."
"We must focus aid on reducing overcapacity, on reducing fuel dependency, and on market measures which can help fishermen raise the first-sale value of their fish," Borg said.
"Only in this way can we help establish a truly sustainable future for the industry."