The arrests came as militants warned of "another bloodbath" and a "long, gruesome war" unless Kenya withdrew its troops from Somalia.
Forensic police officers continued to scour the site where one student shocked security forces by emerging unharmed from a wardrobe where she had hidden for over two days.
A Kenya Red Cross spokeswoman said that the 19-year old was traumatised and dehydrated but physically unharmed and undergoing assessment by doctors.
Thursday's attack on Garissa University, situated near the border with Somalia, claimed 148 lives, including 142 students, three police officers and three soldiers.
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The massacre was Kenya's deadliest attack since the 1998 bombing of the US embassy in Nairobi, and the bloodiest ever assault by the Shebab militants.
Interior ministry spokesman, Mwenda Njoka, said five arrests had already been made.
"Three were the coordinators who were arrested while trying to flee to Somalia, two were arrested within the precincts of Garissa University," he told AFP, noting that the four gunmen in the university were killed on Thursday.
The name of the three suspected organisers were not given, but Njoka said the two arrested on campus included a security guard at the university, and a Tanzanian named as Rashid Charles Mberesero.
"He was hiding in the ceiling of the university and had grenades," Njoka said, while the guard, a Kenyan of ethnic Somali origin, was named as Osman Ali Dagane.
He is suspected of helping the gunmen, and was found "in possession of jihadist materials," Njoka added.
A USD 215,000 (200,000 euro) bounty has also been offered for alleged Shebab commander Mohamed Mohamud, a former Kenyan teacher believed to now be in Somalia and said to be the mastermind behind the Garissa attack.