Italian Ambassador Giacomo Stanfelice would accompany the Marines to Rome, sources said.
The formalities at the Foreign Residents Registration Office (FRRO) office at Nedumbassery airport were completed before they visited the Commissioner's office here.
When reporters asked Stanfelice if they were happy with the process, he said "it was a fair process".
Italian Consul General in India Giampaolo Cutillo said the marines - Latore Massimilliano and Salvatore Girone - would come back to India.
The marines secured their passports from Kollam Additional District sessions court judge T K Madhu by noon today after submitting an unconditional joint undertaking to return to the state by January 10 and appear before the trial court in Kollam on January 15.
They also executed the Rs six crore bank guarantee as directed by the Kerala High court yesterday while granting them permission to leave Kerala for two weeks.
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They had to rush back to Kochi to get other formalities completed, including at the FRRO at Nedumbassery airport.
The Italian Ambassador and Consul General had accompanied them to Kollam.
Yesterday, the High Court had permitted them to leave for Italy on stringent conditions. It was also made clear that the undertakings by the Italian Ambassador and Consul General should be acceptable to the Union government.
Italian Defence minister, Giampaolo Di Paolo was here last weekend to meet the marines.
The Congress-led UDF government today came under attack from Marxist veteran V S Achuthanandan for not challenging the court order, even as CPI(M) youth wing activists staged a black flag demonstration in Kollam protesting against the decision to allow the marines to leave for Italy.