According to multiple sources, Githii was forced to resign "because he was being seen as an obstacle".
"Tension has been high at the board for weeks now. Things have really been tough and today (yesterday) he was told to either resign or be fired," said a source.
The fate of the other commissioners is unknown though sources say they may be deployed to other government agencies.
"Tension is very high here. Most people who were aligned to Mburu are in a panic because they believe they too will be targeted," a senior staff member said.
In a statement, the tax collector's board chairman Anthony Mwaura said Mburu had handed in his resignation letter to pursue other personal interests.
Little was said about the four commissioners whose positions have been handed to new officials, some in acting capacities.
"Following the resignation, the board has appointed...Rispah Simiyu...to be the Acting Commissioner General KRA with effect from February 23 until the position is substantively and competitively filled," Mwaura said.
Mburu was appointed KRA commissioner general on June 6, 2019, to replace John Njiraini who had served in the role since March 2012.
He was plucked from the intelligence wing of the authority at Times Tower to take up the critical post from Njiraini who had left office at the end of his tenure.
During his tenure, KRA's tax revenue collection grew from Sh1.607 trillion in 2019-20 to Sh2.03 trillion in 2021-22 (the first time breaching Sh2 trillion). So far in 2022-23, tax revenue collection has hit Sh1.105 trillion, 53.3 per cent of the targeted full financial year amount.
Mburu, an accounting expert, is now replaced by Simiyu who becomes the country's first-ever female commissioner general, albeit in acting capacity.
Prior to the appointment, Simiyu was the commissioner of domestic tax. Her position is now taken by Pamela Ahago.
Simiyu has worked at the KRA for more than four years prior to her latest appointment. She served as the KRA commissioner from October 2020 where she was responsible for domestic taxes.
She also served as the KRA deputy commissioner from April 2018 to October 2020.
Prior to joining the tax agency, she was the East Africa regional manager of Standard Charted Bank for seven years from January 2011 to April 2018.
Simiyu was also the manager of tax services at PricewaterhouseCoopers for more than nine years from September 2001 to December 2010.
She studied for her Master of Laws in International Trade and Investment at the University of Nairobi from 2008 to 2009, and Bachelor of Laws degree from 1998 to 2001 at the University of Dar es Salaam.
Those shown the door from KRA's management position include Terra Saidamu, who until then was commissioner of Intelligence and Strategic Operations. His position has been handed to David Yego.
Others are David Kinuu, Edward Karanja and Lilian Nyawanda. Most of these commissioners were appointed by Ruto's predecessor, Uhuru Kenyatta.
The Kenya Kwanza government has been systematically weeding out Uhuru's appointees in various state offices, including KRA where it kicked out Kibaki and Uhuru-era chairman Francis Muthaura in favour of Mwaura, the United Democratic Alliance National Elections Board chairperson.
Githii's resignation and subsequent sacking of five commissioners is coming just months after Ruto warned them to either perform or exit.
In November, Ruto said that Kenya’s revenue collection accounts for 14 per cent of the country’s Gross Domestic Product while in other middle-income countries, the figure is as high as 25 per cent.
He lamented about rampant tax avoidance, asking commissioners to correct the mess, or he will do it by himself. "I have told the commissioner general to sort out this mess. If he doesn't, I will sort it out myself,'' Ruto said.
Early this month, the President made new appointments that saw hundreds of Uhuru and Raila Odinga allies kicked out from various parastatal boards.
Recently, his deputy Rigathi Gachagua justified the move, equating government appointments to company shareholding.
Speaking in Kericho on Sunday, Rigathi Gachagua declared that government appointments and contracts are a preserve of those who voted for the Kenya Kwanza government.
He said that their government will reward its staunch supporters and those who toiled to put the current government in office and give the least consideration to members of the opposition.