"The yellow ribbon wrapped around the insignia of the San Marco Regiment Lion, and symbol of the solidarity to the two riflemen Massimiliano Latorre and Salvatore Girone, who were detained in India by local judicial authorities... will be removed today (Wednesday) from the Italian Navy's website," read a message on the website.
Italy has reportedly asked India to set up a meeting of diplomats in order to reach "an amicable solution" over the case of Latorre and Girone, who Rome is refusing to return to India to stand trial for the killing of two Indian fisherman in February 2012.
India has summoned the Italian ambassador in New Delhi to express its anger over Rome's decision, which the Indian government has termed "unacceptable".
India's Supreme Court allowed Latorre and Girone to go home to vote in last month's elections. The marines were ordered to return within four weeks.
Italy argues that because the case is subject to international maritime law, it had been decided that the pair would not return to India when their leave permits expired.
Rome is arguing it wants its nationals to be tried in Italy, saying the incident took place in international waters and that New Delhi does not have jurisdiction in the case.
At the time of the shooting, the marines were guarding the Italian oil tanker Enrica Lexie off India's southwestern coast.
Italy says the Indian fishing boat had "behaved aggressively" and ignored warning shots from the tanker. The fishermen were reportedly unarmed.
Last year, Italy paid compensation of Rs.10 million (around $184,000) to each of the families of the fishermen.