EU politicians waded into the ongoing diplomatic row between Italy and India on Thursday when they approved the motion on the grounds that India holding the pair without charges is a "grave violation of human rights", Ansa reported.
They also called for a swift solution and said the case should be dealt with by the Italian judicial system or go to international arbitration.
Federica Mogherini, the EU’s head of foreign policy, said the high-profile case risked damaging EU-India relations.
"We share values and strategic interests with India and we want to cooperate in the world arena,” she was quoted by Ansa as saying.
"But it's good for everyone to be fully aware of how much of an impact the unresolved dispute of the two Italian Navy officers can have on relations between the EU and India. It is putting them to the test."
Earlier this week India’s Supreme Court allowed one of the marines, Massimiliano Latorre, to stay in Italy another three months to recover from heart surgery.
The court had initially refused to extend the 47-year-old’s leave after allowing him to spend four months at home to recover from cerebral ischaemia - a restricted blood supply that can lead to a stroke.
Latorre and fellow marine Salvatore Girone are accused of shooting the fishermen while serving as part of an anti-piracy mission on an Italian-flagged oil tanker off the southern Indian state of Kerala in February 2012.
Girone is living at Italy's embassy in Delhi.
The Italian sailors say they mistook the fishing boat for a pirate vessel and fired what were intended to be warning shots.
Italy says the pair should be tried on home soil since the shootings involved an Italian-flagged vessel in what it insists were international waters.
India, however, maintains the killings took place in waters under its jurisdiction.
Rome last month threatened to withdraw its ambassador from India after the court rejected the appeal over the leave.
The marines were granted home visits to vote in national elections in 2013, but India was furious when the Italian government initially said it would not send the men back.
A subsequent U-turn, which followed intense Indian diplomatic pressure, triggered the resignation of Italy's then foreign minister.