The Indian court had allowed the marines to go home to vote in last month’s elections.
Ambassador Daniele Mancini had personally assured the court the marines would return by March 22.
On Wednesday, Indian PM Manmohan Singh warned that “there will be consequences” unless Italy returned the marines.
In unusually strong language, Manmohan Singh said that Italy’s refusal to send back the marines was “unacceptable”.
Rome’s decision has come as a major embarrassment for the Indian government and opposition parties have been demanding their immediate return.
On Thursday morning, the court headed by Chief Justice Altamas Kabir issued a notice to the Italian ambassador, restraining him from leaving without its permission.
Daniele Mancini has been asked to respond to the notice by March 18.
India’s Attorney General GE Vahanvati told the judges that Rome’s failure to return the two marines “is a breach of undertaking given to the highest court of the land and the government is extremely concerned about it”.
In February, the Supreme Court allowed Massimilian Latorre and Salvatore Girone to go home to vote in the Italian elections. They were ordered to return within four weeks.
But on Monday, Italy informed India that the marines would not be coming back, prompting a diplomatic row.
The marines are accused of shooting the fishermen in February 2012. They said they mistook them for pirates.
Italy argues that because the case is now the subject of international maritime law, it has been decided that the pair will not return to India “on the expiration of the permission granted to them”.
Rome says that it wants its nationals to be tried in Italy. Because the incident took place in international waters, Italy believes India has no jurisdiction in the case.
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