The Supreme Court had given Massimiliano Latorre leave to spend four months at home after he suffered a cerebral ischaemia – a restricted blood supply that can lead to a stroke – in September.
On Tuesday it rejected Latorre's request to extend his leave and undergo further treatment, saying the legal proceedings must resume.
Latorre and fellow marine Salvatore Girone are accused of shooting the fishermen while serving as part of an anti-piracy mission on an Italian-flagged oil tanker off the southern Indian state of Kerala in February 2012.
The Italian sailors say they mistook the fishing boat for a pirate vessel and fired what were intended to be warning shots.
The court also rejected a plea by Girone, who has been living at Italy's embassy in New Delhi, to be allowed to go home for Christmas.
Italy says the pair should be tried on home soil since the shootings involved an Italian-flagged vessel in what Rome insists were international waters.
India, however, asserts the killings took place in waters under its jurisdiction.
The marines were granted a home visit to vote in national elections last year, but India was furious when the Italian government initially said it would not send the men back.
A subsequent U-turn, which followed intense Indian diplomatic pressure, triggered the resignation of Italy's then foreign minister.
In September, the Italian ambassador gave his personal guarantee that Latorre would return to India to face trial.