The marines will, however, continue to remain in a Kerala jail.
The court accepted the Italian government's assurance that it would ensure the presence of the four other marines on board the ship before any court in India as and when they are summoned.
The four other marines could be required by the investigating officer probing the killing of the Indian fishermen.
"We accept the assurance given by the Republic of Italy that the presence of four marines if required by any court or investigating officer or any lawful authority would be ensured," an apex court bench headed by Justice RM Lodha said, allowing the onward voyage of the ship.
The court also recorded the statement of Italian government that these four marines will have the right to challenge the summons seeking their presence before any competent court.
The court also made it clear that no legal proceedings arising out of the shooting of the two Indian fishermen would come in the way or impede the voyage of MV Enrica Lexie.
The court also noted that the Indian government does not accept the correctness of the assertion made by the Italian government in its statement before the apex court that the incident occurred in international waters.
It also noted that the Kerala government had vehemently opposed the Italian government's statement, saying it was not acceptable.
The centre and the Kerala government have said that the Italian government's statement would not prejudice the legal proceedings arising out of the Feb 16 incident.
Two Italian marines, Chief Master Sergeant Massimilano Latorre and Sergeant Salvatore Girone, are in judicial custody since Feb 20 and are lodged at the Thiruvananthapuram Central Jail.