Kenyatta "expressed deep concern over the sharply deteriorating situation" in North Kivu where fighting has broken out "between various armed groups, the Armed Forces of the (Democratic) Republic of Congo (FARDC) and the M23," his office said in a statement.
The statement was released a day after Rwanda fired at a fighter jet from the DRC that the government in Kigali claimed had violated its airspace.
Kinshasa denied one of its aircraft had flown over Rwanda, and accused Kigali of an attack on the jet that it said amounted to "an act of war."
The DRC - along with the United States and several European countries - has repeatedly accused Rwanda of backing the Tutsi-led M23 rebels, although Kigali denies the charge.
Kenyatta made no reference to the warplane incident but called for "cessation of all hostilities" and adherence to peace talks in the Angolan capital Luanda and Kenya's Nairobi that unlocked a truce.
"Expressing serious concerns for the targeted killings of civilians by armed groups and thousands of internally displaced people resulting from the two days of fighting in the region, the facilitator has once again called for the cessation of all hostilities," the statement said.
Kenyatta is mediating in the conflict in the volatile region on behalf of the seven-nation East African Community (EAC) bloc.