The case, registered by the NIA in April 2011, relates to transfer of money from Pakistan to Jammu and Kashmir through Hawala channels via Delhi which was suspected to be used in funding terrorism and secessionist activities.
An NIA spokesperson said in a statement, "He was summoned for questioning to Delhi on Tuesday after initial rounds his role was conclusively established in the case and so we arrested him".
Sources say Yousuf accepted money transferred through Western Union by Aijaz, who is on the run, and investigators have documents from Saudi Arabia and India confirming the transfers.
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The NIA has also registered two others cases related to terror funding - one in November 2011 and another in May this year.
Shahid, who lives with his family in Soibugh village of central Budgam district, has a masters degree in agriculture and works as a village agricultural assistant in the state's agriculture department. He will be arrested soon, said a senior NIA official.
"Shahid over the years has been receiving and collecting funds through global wire money transfer from" Hizbul Mujahideen militant Aijaz Bhat, a Srinagar resident now based in Saudi Arabia, an NIA statement said.
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Besides heading terror outfit Hizbul Mujahideen, he is also the chairman of United Jehad Council (UJC), a conglomerate of various terrorist outfits operating in the Kashmir Valley. The Hizb founder's son, according to an NIA official, received at least four instalments of money in 2011, 2012, 2013 and 2014. The other two namely Mohammad Maqbool Pandit and Aijaz Ahmad Bhat are still absconding.
The detention comes a day after the Centre announced the appointment of a special envoy to carry forward the channel of communication in Jammu and Kashmir. The NIA is an autonomous agency, Singh reiterated, suggesting that the talk process will not stall any of the investigations that are underway.
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