The NIA had on July 9 filed a case against Ansarulla under various sections of the Indian Penal Code and the Unlawful Activities (Prevention) Act after it learnt that members of the group had collected funds and made preparations to carry out terrorist attacks in India.
On Saturday, it raided multiple locations in Tamil Nadu on a tip-off that some people were conspiring to wage a war against India.
Other than the residences of Ali and Mohamed, the NIA also searched the homes and offices of others, including one Syed Bukhari in Chennai.
Nine mobiles, 15 SIM cards, seven memory cards, three laptops, five hard discs, six pen drives, two tablets, three CDs/ DVDs as well as a large number of documents, including magazines, banners, notices, posters and books were seized in these searches.
"Based on incriminating facts revealed during the searches in Nagapattinam as well as Chennai in Tamil Nadu, and subsequent investigation accused Hassan Ali and Harish Mohamed were arrested on Saturday," said an NIA official.
"They will be produced before a special NIA court in Chennai this afternoon. Bukhari is still being examined," he added.