Police will be sent to all public universities and colleges to tear down terrorism networks there.
Deputy Secretary for internal security Thomas Sakah said on Tuesday universities have become centres of radicalisation and recruitment by extremists and terrorist organisations.
"A number of university students have been reported missing only to be traced in Somalia or Syria where it is believed they are training with the Al-Shabaab or Isis for deployment in Islamic Caliphates," he said.
He was addressing new university council members during their orientation in Naivasha.
A number of university students are said to be members of organised crime gangs carrying out armed robbery, carjacking, cybercrimes, drug trafficking and terrorism.
According to the Commission for University Education, more than 44 students -- 17 of them girls -- from public and private universities joined terror groups last year to fight in Somalia and Libya.
The terror groups are recruiting the best brains in universities such as those pursuing medicine, engineering, law, nursing and psychology.
He said Abdirahim Abdullahi, who was involved in the 2015 Garissa University terror attack in which more than 148 students died, was a lawyer trained at the University of Nairobi.
Mr Sakah said the institutions had become terror targets due to their low capacities for armed resistance, lack of preparedness and surprise element.
"Un-ethical hackers have been reported to intrude into systems of government institutions, public universities and private organizations for various reasons. Hackers have the capacity to intrude into insecure university administration systems and to alter examination marks, grades of students and financial fraud," he said.