Mr Justice George Odunga issued the order on Friday after activist Okiya Omtatah sued the NGO Coordination Board.
Claims that IFES is not registered as an NGO, Mr Omtatah argued, are unfounded.
He said IFES is registered as a Trust under the Lands ministry and denied claims that the NGO is a company.
Judge Odunga consequently suspended the NGO board order and agreed to certify the matter as urgent.
NGO Coordination Board Executive Director Fazul Mahamed on December 19 stopped IFES’s Sh2 billion elections programme, saying the entity was operating illegally.
The NGOs board said that the employees of IFES had not been registered by them nor had they obtained a work permit from the Principal Immigration Officer, who was also copied in the letter.
This was a week after President Kenyatta claimed foreigners were pumping in billions of money “in the guise of civic education”, but funds he said were meant to influence regime change.
IFES has funded NGOs to actively participate in the electoral process by voter registration, civic education, capacity building, and advocacy for women and youth participation in elections, consensus building and early conflict response.
USAid, the funder of IFES, has denied Mr Fazul’s and President Kenyatta’s claims.