An NIA spokesman said Shahid, 42, who is employed with the Department of Agriculture of the Jammu and Kashmir government, was summoned to the agency's headquarters, and was arrested after questioning with regard to allegedly receiving money from his father.
He will be produced before a designated NIA court tomorrow.
The NIA has alleged that Shahid had received funds through a US-based international wire transfer company from Aijaz Ahmed Bhat, another accused in the case who is absconding and based in Saudi Arabia.
The NIA claimed so far that he had received a total of nearly Rs 4.5 lakh through eight international wire transfers.
The case, registered by the NIA in April 2011, relates to the transfer of money from Pakistan to Jammu and Kashmir through hawala channels via Delhi, which the agency believed was used in funding terrorism and secessionist activities.
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The agency had filed a charge sheet against 10 people including Syed Salahuddin in the April 2011 case.
In the recent case, the NIA arrested 10 people, including some close relatives and aides of Geelani.