Acting Treasury Cabinet Secretary Ukur Yatani and his Principal Secretary Julius Muia have taken over at the ministry.
Head of Public Service Joseph Kinyua introduced the two to the staff on Thursday, a day after they were appointment to the positions.
President Uhuru Kenyatta named Mr Yatani to replace Mr Henry Rotich, who was arrested on Monday on abuse of office allegations.
The Head of State also fired Treasury Principal Secretary Kamau Thugge, a day after he was arraigned together with CS Rotich over the Arror and Kimwarer dams scandal and freed on bail.
In the mini-reshuffle, Dr Julius Monzi Muia who headed the defunct National Economic and Social Council and the Vision 2030 was appointed National Treasury PS.
Mr Yatani, who is the Labour CS, said he would focus largely on the Big 4 Agenda.
He added that he would soon come up with the work strategy and set timelines.
The CS said the limited resources would be "deployed in the right manner and never misappropriated."