Italy recalled its ambassador to India to Rome for consultations after the charges were laid against Latorre Massimiliano and Salvatore Girone by a chief magistrate in the coastal city of Kollam in Kerala.
Official sources in New Delhi confirmed that Italian Ambassador Giacomo Sanfelice di Monteforte was called back by his government, a report by the Press Trust of India said.
Italian Deputy Foreign Minister Staffan de Mistura met with the two naval guards last week and expressed concern over the lengthy judicial process in India.
The men are being held in prison in the Kerala state capital Trivandrum.
De Mistura said the killing of the fishermen was "accidental" and insisted that Indian courts didn't have jurisdiction over the incident, the PTI report said.
The incident Feb. 13 sparked an immediate flurry of exchanges between Italian and Indian diplomats when Indian authorities took the two Italian marines into custody.
The two Indian fishermen, aged 25 and 45, were killed around 14 miles off the Kollam coast of the state of Kerala, southern India, when two armed guards on the Italian-flagged oil tanker Enrica Lexie allegedly fired at the fishing boat.
Preliminary assessment by marine authorities is that the guards might have mistaken it for a pirate vessel, a report by the PTI said at the time.
Rome had said it wanted to take legal action against the two guards under U.N. Conventions and invited India to act as an interested party, something which New Delhi is against, a report by the television station IBN Live said.
Indian authorities see the issue as an internal matter and the Italians likely will be tried in an Indian court under Indian law.
The Italian government reportedly has offered to pay around $190,000 to the families of both the dead fishermen and in return the families would withdraw the court cases.
A hearing this week will set a start date for the trial.
India has capital punishment but the country's Supreme Court ruled in 1983 it should be imposed only in exceptional cases. The killers of India's independence leader Mahatma Gandhi and of Prime Minister Indira Gandhi are among those executed.
The last prisoner executed in India was Dhananjoy Chatterjee who was hanged in August 2004 for the rape and murder of a schoolgirl in 1990.