Education Cabinet Secretary Amina Mohamed has sent Meru University Vice Chancellor Japheth Magambo on terminal leave pending expiry of his term in June.
Ms Mohamed made the announcement when she visited the troubled university in Meru County on Tuesday.
She said Prof Charity Gichuki would take over the running of the university of science and technology in an acting capacity.
The CS ordered the university, which was shut following deadly student riots, reopened in a week’s time.
Ms Mohamed said the university council had agreed that Prof Magambo take leave pending the expiry of his contract in June.
Mr Njoroge, who is set to be buried this week, was gunned down at close range on February 27 as he attempted to flee from police.
Ms Mohamed, who was accompanied by Education PS Micheni Ntiba, called on police to fast-track investigations into the killing of the student leader.
“I convey my condolences to the family and friends of the late Njoroge. We regret what happened. The police should conclude investigations in time to give rest to the family,” she said.
“As a ministry, we have resolved to engage student leaders and university managers to address issues before they erupt.”
She urged the university’s council to work closely with the acting VC to ensure learning resumes in the next one week.
“The council and management should engage other stakeholders, including the community, on a regular basis. We thank Prof Magambo for the many years of service after he took over the institution when it was a collection of tents,” she said.
Council Chairman Dulacha Galgallo assured students that their issues would be addressed.
“I urge the students to find redress through dialogue and comfort in the changes. I urge the student leadership to work with the acting VC in addressing all the issues internally,” he said.
“As a council, we are ready to support them and make their stay here comfortable.”
He said he was ready to spearhead dialogue with the students to ensure uninterrupted learning.
The CS later addressed some students outside the university and assured them of the government’s resolve to address their issues.
A preliminary post-mortem report on Mr Njoroge’s body indicated he was shot “on contact” using a pistol.
Family pathologist, Dr Moses Njue, said the student leader was shot in the back of the head. The bullet exited through the ear, causing instant death.
Various leaders, including Njuri Ncheke elders and the Meru university staff union, had called for the removal of Prof Magambo.