The court went on to allow the government to proceed with the NIIMS process which President Uhuru Kenyatta is set to officially launch in Machakos county on April 2, 2019.
The government had launched a pilot programme of NIIMS on February 18, which was carried out in 15 counties.
However,the government has been barred from forcing Kenyans to register.
On Monday, the High Court has also barred the government from using the data to withhold any services or bar anyone from accessing public facilities.
In addition, the 3-judge bench ruled that the collection of DNA and GPS coordinates was suspended from the exercise.
“The State is prohibited from including DNA in the biometrics,” the court ruled.
The suit was filed by the Kenya Human Rights Commission (KHRC), Nubian Rights Forum, and the Kenya National Commission on Human Rights (KNCHR) was heard on Friday.
According to the three bodies, the condition that no one will access government services without a Huduma Namba is a violation of fundamental rights protected under the bill of rights.
They argued that public services should not be pegged to documentation and that communities like the Kenyan Somali and Nubian risk further marginalization.