Statehouse Chief of Staff is facing a huge opposition within the powerful house on the hill.
On top of the various accusations is that of influencing top appointments, with critics pointing at Inspector General of Police Hilary Mutyambai and others from his Ukambani backyard.
But a top official defended the appointment of the new police chief, and said Waita did not play any role.
“We know how and why Mutyambai was arrived at. They should not link him to Waita simply because they are both Kamba,” said the source.
Mutyambai beat out at least four other candidates whose names had been forwarded to the President for appointment.
They included National Intelligence Service (NIS) Senior Officer in Charge of Border Control, Frontier, Nicodemus Musyoka Ndalana, former NIS official and current Kenya Ambassador to Brazil Isaac Ochieng, and police spokesman Charles Owino.
Insiders add that Waita has had a strained relationship with his deputy Muturi and other senior officials at State House.
While serving as the Solicitor General, Muturi was also accused of fighting with his boss, then Attorney General Githu Muigai. He also served as Uhuru’s personal assistant.
Waita’s drama is said to have worsened last August, when Kenya Railways Business Research General Manager Philip Mainga was appointed acting managing director of Kenya Railways Corporation (KR) following Atanas Maina’s suspension.
Mr Maina is among those who were suspended over alleged irregular payments of SGR compensation.
When Mr Mainga was named acting KR boss, some officials accused Waita of being behind the move.
“He has been facing a barrage of accusations, with some insiders claiming he only pushes for appointments for people known to him,” said one official aware of the intrigues.
Waita joined the Government in 2016 and has been at the centre of key decisions.