Italy's foreign minister has resigned over the case of two Italian marines charged with killing two fishermen in India.

Giulio Terzi, 66, announced his decision to step down during parliamentary questions on the case, saying he disagreed with the government's decision to send the marines back to India.

"My voice was left unheard," Terzi told the Parliament. "I resign because after more than 40 years [in the diplomatic service] I believe Italy's honour and that of its armed forces and diplomacy should be always defended.

"I resign because I'm sympathetic with the two marines and their families."

Terzi has been widely criticised for the confused handling of the issue that triggered a diplomatic row between Rome and New Delhi.

Tension between the two countries escalated this month, as Italy reneged on its commitment to return Massimiliano Latorre and Salvatore Girone to Indian authorities after the two were given licence to vote in Italy's national elections and celebrate Easter at home.

Delhi barred Italian ambassador Daniele Mancini from leaving the country, before Rome eventually overturned its decision to block the marines' return.

Terzi's resignation highlighted infighting in Prime Minister Mario Monti's government on the management of the case.

"It's easy to resign now but I won't do it," said defence Minister Giampaolo Di Paola, addressing the Parliament after Terzi.

"[Terzi's] analysis and views are not shared by the government."

Latorre and Girone were part of a security team aboard a cargo ship when they began shooting at a boat they claim they mistook for pirates, off the coast of Kerala.

The two marines were arrested in Kerala and a row on where they should stand trial began.

The Italian government claims the offence took place in international waters, and thus the pair should be tried in Italy under international maritime law. However India maintains it has jurisdiction over the case.