Hundreds of demonstrators waving placards and chanting slogans marched on the streets of the capital Nairobi and the northeastern town of Garissa, where the massacre was carried out.
Security forces meanwhile continued their hunt for those behind the university killings.
In Garissa, several hundred people gathered at a rally where both Muslim and Christian leaders called for unity, with local Muslim leader Abdullahi Salat condemning the "violent and evil attack".
Maureen Mucheri, 21, an engineering student at Nairobi University, said she feared another attack, refusing to go into shopping malls and churches, because "the government is doing nothing".
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Some students carried flowers, others stopped to light candles.
"We are mourning the loss of our fellow comrades, we have lost the vibrant blood that would have built tomorrow's Kenya," Mucheri added.
A vigil is planned for early evening on the third and final day of national mourning.
Special forces units took seven hours to reach the university in Garissa last Thursday, some 365 kilometres from the capital, as Shebab gunmen stormed dormitory buildings.
The extremists lined up non-Muslim students for execution in what President Uhuru Kenyatta described as a "barbaric medieval slaughter".
Students in the demonstration carried placards with the slogan "147 is not just a number", referring to the death toll in the massacre - although that has since risen to 148.