A bench headed by Chief Justice J S Khehar said the investigation into the matter will be supervised by the retired apex court judge R V Raveendran.
It directed the probe agency to furnish the report to it after completing the investigation.
The apex court bench, also comprising Justice D Y Chandrachud, said it will take a view after considering the NIA's probe report, inputs from the Kerala Police and after talking to the woman.
On August 10, the apex court had asked the Kerala Police to share the probe details of the case with the NIA.
The issue reached the apex court as Kerala-native Shafin Jahan challenged the annulment of his marriage by the Kerala high court which ordered the state police to probe such cases.
The top court had said that it was entrusting the task to the National Investigation Agency as a neutral agency to get a "whole picture" and ascertain whether the particular instance was limited to a "small pocket" or was there "something wider" to the issue.
Jahan, who had married a Hindu woman in last December, had moved the apex court after the Kerala high court annulled his marriage, saying that it was an insult to the independence of women in the country.
The woman, a Hindu, had converted to Islam and later married Jahan.
It was alleged that the woman was recruited by Islamic State's mission in Syria and Jahan was only a stooge.
Earlier, the apex court had sought a response of the NIA and the Kerala government on the plea of Jahan.
Ashokan K M, the father of the woman, had alleged that there was a "well-oiled systematic mechanism" for conversion and Islamic radicalisation.
The NIA has recently conducted probe into some cases of 'love jihad' in which women were allegedly being sent to Syria to join the Islamic State.
The high court, while declaring the marriage as "null and void", had described the case as an instance of 'love jihad' and ordered the state police to conduct probe into such cases.
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