Malik, who had warned to launch a protest against the NIA in Delhi, was nabbed from his Abi Guzar office in Srinagar.
NIA raid at residence of Hurriyat's Aga Hassan in Budgam District.
The offices of the CA of arrested Kashmiri businessman Zahoor Wattali and residences of some cross-border traders were also searched. Both Mr. Alsafvi and Mr. Sumji are associated with the Hurriyat led by Syed Ali Geelani.
The NIA conducted raids at 12 places in the Valley and at one place in Jammu city.
The arrest comes a day after the Joint Hurriyat leadership of Kashmir announced to hold a day long protest in New Delhi outside the headquarters of National Investigation Agency (NIA) over arrests and warrants against dozens of hurriyat leaders since last few months. The NIA is reported to have seized Rs. 2.2 crore in cash during the raids and also detected "suspicious" foreign transactions of about 100 crore during the investigation. The house of another of Mr. Shah's associates, Choudhary Razak, in Jammu was also searched.
Malik was arrested from his Maisuma residence and later lodged in central jail Srinagar.
Meanwhile, the authorities placed Mr. Geelani and the Mirwaiz under house arrest. The NIA can record the statement of a witness at his place of residence if he is less than 15 or more than 65 years of age.
The agency had in July arrested seven separatist leaders and a prominent local businessman in connection with the probe into the terror funding by Pakistan-based terrorist groups to stoke unrest in the valley.
On Wednesday, two men, including a freelance photo-journalist, arrested yesterday for alleged stone-pelting in Kashmir Valley and mobilising support against security personnel through the social media, were on Wednesday sent to 10-day NIA custody for interrogation.
Lawyers in the valley have made a decision to stay away from courts till Qayoom returned from Delhi.
"We are analysing the documents collected from the NIA and planning to register a PMLA and FEMA case against the separatist leaders", the ED official said.