Yazda said Iraqi-Kurdish security forces closed the office in Duhok for "unknown reasons" on Monday, and workers were told that all humanitarian projects to Iraq's Yazidi community had ended, Rudaw reported.
Human Rights Watch said three men from the ruling Kurdish party's militia told the NGO workers in Duhok on Monday morning that Yazda was "closed" and padlocking the doors of the office.
The group believes the decision stems from Yazda's plans to provide essential materials to 3,000 Yazidi families living in Sinjar, where a strict blockade has been imposed by Kurdish authorities.
Human rights groups have voiced concern about the restrictions on basic goods entering the Sinjar region, leading to worryingly dire conditions for the local Yazidi population.
Yazda provides medical care, pyschological support, training and education to Iraq's ethnic and religous Yazidi community, which was traditionally situated around the Sinjar Mountains.
An offensive by the IS in northern Iraq saw thousands of women and children forced into sex slavery by the group, while men, the sick and elderly were murdered.
Yazda aims at raising awareness of these acts of genocide against the Yazidi and document the murders and abuses against the community so the perpertrators can be brought to justice.
UN goodwill ambassador Nadia Murad - herself held captive by IS militants - works with the group and called for the NGO to be reopened.
"I call on the [Kurdistan Regional Government] to reopen Yazda vital work without any delay. Its shame to close the [organisation] that supports my campaign," she tweeted.
Officials from the regional Kurdish government told Rudwa that Yazda was closed for engaging in "political activities" and had been warned prior to the clampdown. Yazda workers deny the claim.
Kurdish militias have been criticised for the mismanagement of Yazidi mass graves and turf wars, with human rights groups telling The New Arab in 2015 it could make the documentation of the mass killings difficult or impossible.