High Court judge James Makau has declined to stall Treasury Cabinet Secretary Henry Rotich's presentation of the 2019-20 budget statement.
In a ruling on Thursday, the judge said the process of doing so would be against public interest since it is long.
The Kenya Human Rights Commission, Transparency International, Africa Centre for Open governance (Africog) and the Institute for Social Accountability (Tisa) on Thursday filed the case in Nairobi, a few hours to Mr Rotich’s speech in Parliament.
They argued that the budget could not be tabled in the House before approval of the Division of Revenue Bill.
The lobbies said that since the bill dictated the sharing of revenue between the two levels of government, it would be impossible for counties to deliver.
They sued the Attorney-General and CS Rotich and listed the Council of Governors as an interested party.
In his ruling, justice Makau noted that the rights groups filed the case on the day of the presentation of the budget.
He allowed the objection by the Attorney-General, who had said the move was ill-advised.
Mr Makau also noted that the case was filed at the Machakos High Court and then transferred to Nairobi.
He scheduled a hearing for July 2.