The ambush at the Isiolo-Garissa border, which claimed the lives of two children and a suspected raider, was retaliatory, the government has said.
An unknown number of armed attackers believed to be from Isiolo raided villages in Janju at around 6am on Tuesday.
The victims were identified as children aged 11 and 13, and a suspected raider. Other reports, however, indicated that the man was a police reservist.
Isiolo County Commissioner John Ondego said the attack was instigated by three that occurred at the weekend.
Two pastoralist communities from Isiolo and Garissa have been fighting over pasture and the boundary between the counties.
Two people were shot dead and another injured on Saturday in a clash between armed groups from the two counties at Uchana, Isiolo.
On Sunday morning, two people were wounded during a botched cattle raid at Mata Bofu, Isiolo, by suspected rustlers from Lagdera.
A few hours after the botched raid, one person was injured when fracas erupted at Modogashe livestock market.
Mr Ondego said, “Bandits from both counties have been engaging in retaliatory attacks since Saturday’s incident. Despite the government’s move to end the fights through dialogue, the attacks recur."
Security officials believe the attacks were the result of a border row.
Two hundred and fifty internally displaced persons, who fled Eldera in July over land wrangles and settled in Garba Tula town, were supposed to return to their homes on Saturday when the first attack occurred.
However, Garissa County commissioner Joshua Chepchieng said criminal elements are using "imaginary boundary conflicts" to raid neighbouring villages, kill and steal livestock.
"Modogashe has been a business hub for both communities. They have co-existed since Kenya's existence. We call for local political, opinion and religious leaders to preach peace among these communities," he said.
Mr Chepchieng said police were in hot pursuit of the killers as every Kenyan has a right to live anywhere.
"Its very wrong to kill another. These communities have been living together peacefully for years. Claims that these killings are as a result of boundary disputes are not true. It's simply a case of criminals taking advantage [of circumstances]," he told Daily Nation in his office on Tuesday.
The commissioner and other senior security officials held a crisis meeting that lasted hours.
Mr Chepchieng said more police officers were deployed to the area and that investigations would lead to the arrest of suspects.
He denied allegations that police reservists from both sides were issuing guns to attackers.
"We have taken the fingerprints of the man alleged to be a raider. We will establish whether he is police reservist as claimed," he said.
The attacks have gone on for months but nobody has been charged with murder.
But the government has warned individuals from both counties, who incite members to fight, that they will be arrested and punished in line with the law.
Mr Ondego asked the parties to allow candidates of the Kenya Certificate of Secondary Education (KCSE) examinations a peaceful season. The attacks, he noted could cause fear among them.
The affected area has only one examination centre. Education and security officials confirmed that the attacks had not disrupted the process.
Isiolo political leaders led by Governor Mohamed Kuti and Isiolo South lawmaker Abdi Koropu Tepo on Tuesday said it is time for peace talks to end the bloodshed.
The two, who spoke during the launch of a fire engine at Kiwanjani, Isiolo town, said an inter-county security meeting is necessary as innocent people are suffering.
Garba Tula Deputy County Commissioner (DCC) Victor Kamonde said local security personnel and those from Lagdera in Garissa were sent to beef up security and restore calm.