Justice Onesmus Makau has set aside his earlier suspension of the fresh vetting of all procurement officers.
In a ruling on Wednesday, Makau noted that an employer has the right to send employees on compulsory leave.
"Such employees will not suffer any prejudice because they will still earn their salaries," he said.
Makau temporarily suspended the vetting in a ruling on June 6, following a suit by activist Okiya Omtatah, who objected the contents of a notice by Head of Public Service Joseph Kinyua.
An independent consulting firm will be engaged to work with the Public Service Commission to vet public service officers targeted in the war on corruption.
The government will head-hunt a reputable company that will conduct polygraph tests on procurement and accounting officers of state agencies, departments and parastatals.
President Uhuru Kenyatta ordered the fresh vetting in his Madaraka Day speech on June 1.
He also asked the officials to step aside and submit their personal information to Kinyua ahead of the vetting.
The notice Kinyua issued on June 4 stated that the information includes certified copies of mobile money statements of the officers and their spouses for a period of six months, and three-year income tax returns for they and their businesses for the last three years.
After Makau suspended the vetting, State House attacked courts, Chief of Staff Nzioka Waita saying it showed that "agents of impunity have found refuge in courts to curtail justice".