Special judge Rakesh Syal allowed the agency to question Shah, Zahoor Watali, an influential businessman who allegedly has close friendship with Pakistani politicians and Kashmiri separatists, and Naval Kishore Kapoor, a UAE-based businessman.
Watali and Kapoor are in judicial custody on charges of funding terrorist activities. They are lodged inside Tihar jail.
The court said the ED would get three days between March 24 and April 5 to quiz them.
NIA had earlier filed a charge sheet against the accused, including Hizbul Mujahideen head Syed Salahuddin, in the case accusing them of "conspiring to wage war against the government" and fomenting trouble in the Kashmir Valley.
The investigating agency has charged Pakistan-based terrorists Saeed and Salahuddin, besides 10 others with criminal conspiracy, sedition, and under stringent provisions of the Unlawful Activities (Prevention) Act.
Earlier on Tuesday, the Enforcement Directorate attached 13 assets located in Jammu and Kashmir in connection with a terror funding case against Hizbul Mujahideen chief Syed Salahuddin.