"I am not taking it lightly," President Ruto said.
"I am taking responsibility that as president this should not have happened. And certainly, some people who are responsible for this failure on the part of government will have to give an account." he said in a joint interview with Kenyan news outlets late on Sunday.
"It should not have happened when we have all the agencies. We have our intelligence, we have our CID (Criminal Investigations Department), we have chiefs and all the other people in the whole of that ecosystem."
Authorities accuse Paul Mackenzie Nthenge, leader of the Good News International Church, of ordering his followers to starve themselves and their children to death so they could go to heaven before the end of the world.
The death toll so far stands at 201, making it one of the worst cult-related disasters in recent history.
Of the 201, eight people died from emaciation after being rescued, while the rest have been exhumed mostly from mass graves in Shakahola Forest in Kilifi County in the country's southeast.
Given the presence of government agencies in the area, including police, intelligence services and the local administration, Mackenzie Thenge's activities should not have gone unnoticed, Ruto said.
Mackenzie Thenge was arrested earlier this year on suspicion of the murder of two children by starvation and suffocation, but was then released on bail.
Relatives of his adherents say that after Mackenzie was freed he returned to Shakahola forest and moved forward his predicted date for the end of the world from August to April 15.
Last week, a court denied bail to the accused. He has not yet been required to enter a plea after handing himself over to police last month.
Ten days ago, Ruto appointed a commission of inquiry into the deaths in Shakahola, and another task force to review regulations governing religious organisations.