Ruto said he was "deeply concerned that members of the diplomatic community have been targeted and civilians in general have been caught in the crossfire."
The Kenyan president's remarks came as Sudan's deadly fighting entered day five following a failed 24-hour cease-fire on Tuesday.
"Kenya notes that disregard for the resolutions coupled with the evidence of lack of commitment to ending the conflict strongly indicates that attacks on diplomatic installations and personnel as well as targeting of hospitals, hotels and other vital public and social spaces are deliberate, systematic and tantamount to atrocities against humanity," he said.
Nearly 300 people have been killed in the past five days, the United Nations health agency, the World Health Organization said, but the toll is likely higher, since many bodies have been left in the streets, unreachable because of clashes.
"There is real danger that the escalation of hostilities in Sudan could implicate external regional and international actors, and degenerate into a security and humanitarian crisis on a disastrous scale," Ruto said.
"It is time to silence the guns in our region and continent," the Kenyan leader added.
On Wednesday, Sudan’s military council and its paramilitary Rapid Support Forces (RSF) made fresh attempts at a 24-hour cease-fire after a failed truce on Tuesday.
Both sides separately announced that they would abide by the new halt in fighting that took effect Wednesday evening.
Residents reported that sporadic gunfire and explosions could still be heard, pointing to the fragility of the efforts.
