Daniele Mancini was ordered back to Rome for consultations, the Hindu reported.
"Italy intends to maintain and intensify its efforts at having its rights as a sovereign state recognized in accordance with international law," Italy's foreign minister, Emma Bonino, said.
An unnamed adviser to India's External Affairs Ministry told the newspaper he is "mystified" by Italy's action and said it seemed like "political grandstanding."
Massimilliano Lattore and Salvatore Girone were stationed on board a tanker that got into a confrontation with a fishing boat off the coast of Kerala in southern India in February 2012. The marines said they believed the boat to be a pirate vessel when they fired, killing two men, because the boat ignored warning shots and approached in a threatening manner.
Earlier Tuesday, the Indian Supreme Court postponed a decision on which law will be used in the trial. The Italian government argues the shooting occurred in international waters, and the marines should be tried in Italy.
The External Affairs Ministry wants the marines charged with offenses that would spare them a potential death penalty. The Home Ministry argues for a trial under the Suppression of Unlawful Acts law, an anti-terrorism statute, the Press Trust of India reported.