A total of Sh2 billion has been set aside to support government sponsored students in private universities this year.
University funding board chief executive Milton Njuki said the money would be paid for students based on the course they are pursuing.
At least 17,368 students were selected to join private universities by the Kenya Universities and Colleges Central Placement Service, the statutory body tasked with admitting students to higher education.
However, Mr Njuki could not disclose the number of students who reported to private institutions in September, saying the body is yet to receive returns.
He disclosed that the use of Differentiated Unit Cost (DUC) had brought transparency and accountability in allocation of funds.
"Previously you could not tell how funding of students was being done, but with DUC, everything is clear now," he said.
Under DUC, student funding is based on courses they take at universities.
Mr Njuki also disclosed that half of students who were selected to join private universities under the government-sponsored programme last year declined the offer.
Only 6,318 out of 12,096 students joined the private universities they had been selected to, he said.
The government initiative to fund students joining private universities was launched last year because a big number of students were missing admission slots in the 31 public universities.
Mr Njuki said that at inception, Sh441 million was used to pay fees for students who joined 22 private universities. "These students are now in their second year of studies in these universities," said Mr Njuki.
Last year, the government set aside Sh700 million for the same purpose.
The CEO said that most of those who did not take up their chances in private universities claimed the degree programmes were inferior. Others cited higher fees in those institutions while others decided to join public universities under self-sponsored programmes.
Last year, parents of students who were admitted to the United States International University (USIU)-Africa under the programme held a protest march after the institution increased the fees. This year, the institution bowed out of the programme.
Like last year, Mount Kenya University admitted most students at 2,905, followed by Kabarak at 1,286 and Catholic University 1,104 students.