Haki Africa head Khalid Hussein described the ruling as bittersweet.
The court case has attracted much attention in Mombasa.
Last month, the accounts of Haki Africa and Muslims for Human Rights (MHR) were frozen on the orders of the central bank and The Commission on Financial Regulation.
The NGOs have accused security agents of being behind the recent assassination of several radical Muslim preachers around Mombasa.
Kenyan officials deny involvement in the killings.
Kenya’s government in December said it had De-registered 510 NGOs, including 15 suspected of having links with terrorism.
Al-Shabab is headquartered in Somalia, but has recruited fighters in Kenya and has carried out a wave of attacks in the country.
despite all this Mombasa high court in Kenya has barred the government from declaring two prominent non-governmental organizations terrorist groups.
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