Treasury CS Henry Rotich and PS Kamau Thugge have been granted Sh15 million bail each.
They have an option of depositing Sh50 million bond.
Justice Douglas Ogoti ordered them to surrender their passports in 48 hours.
The state officials have also been barred from accessing their offices.
They are accused of consipracy to defraud government, failing to comply with procurement law and irregular procurement of insurance policy through single sourcing for the Arror and Kimwarer dams project.
Ogoti said there is a trend that the more the money in question lost the higher the bail terms should be.
Tender committee members for the dams projects and Nema director general Geoffrey Wakhungu were released on Sh750,000 bail.
PS Susan Koech, another suspect, was released on Sh6 million bail with an option of Sh30 million bond.
The prosecution was led by Taib Ali Taib.
He had proposed the accused surrender their passports and travel documents.
Taib had said the bail terms should be commensurate with the billions lost.
The defence agreed with all the proposals, except the suggestion that bail terms be billions of shillings.
Rotich’s lawyers include Kioko Kilukumi, Katwa Kigen, Jinaro Kibet, Mahat Somen and Phillip Nyachoti.
Kilukumi asked the court to release the accused on reasonable bond terms.
He said unless there are compelling reasons, the accused should be immediately released on bail.
Kilukumi said Rotich has fully cooperated with the police and went to DCI headquarters on seven different occasions to help investigators with the case.