According to the NIA, Yousuf, 42, who works in the agricultural department of the Jammu and Kashmir government, was called to the NIA's headquarters where he was arrested after questioning yesterday.
The NIA said Yousuf used to get money through a US-based international wire transfer company from Aijaz Ahmed Bhat, another accused in the case who is suspected to be hiding in Saudi Arabia.
The NIA said Yousuf was "one of several Indian contacts of Bhat" who had been in touch with him for receiving money. The probe agency has said that so far Yousuf has received Rs 4.5 lakh through eight international wire transfers.
The case, registered by the NIA in April 2011, relates to transfer of money from Pakistan to Jammu and Kashmir through hawala via Delhi, which the agency claims was used in funding terrorism and secessionist activities.
The Interpol has alerted the authorities across the globe to look out for them. Yousuf's father was declared a Specially Designated Global Terrorist by the US State Department in June this year.
Besides heading Hizbul Mujahideen, he is the chairman of the United Jihad Council, an umbrella body of terrorist groups operating in Kashmir Valley.