With hundreds of people still thought to be missing, the search operation in the Shakahola forest in southeastern Kenya had been suspended for a few days because of bad weather but has now restarted, Kindiki said during a visit.
"We have many more graves in this forest, and therefore it leads us to conclude that this was a highly organized crime," Kindiki told reporters.
He said on Twitter post-mortem examinations on 112 bodies exhumed or recovered from Shakahola had been concluded. Search and rescue efforts for people "suspected to be holed up in the thickets and bushes have been going on."
Paul Mackenzie, leader of the Good News International Church, has been detained and accused of ordering his followers to starve their children and themselves to death so they could go to heaven before the end of the world, which he predicted was going to happen on April 15.
Mackenzie has not yet been required to enter a plea to any criminal charges. Two lawyers acting for him have declined to comment on the accusations against him.
President William Ruto on Friday announced an inquiry into the mass deaths, while a court kept Mackenzie in detention pending further investigations.
Last week a court released on bail prominent televangelist Ezekiel Odero, whom authorities had said they suspected of being involved in the mass killing of his own followers.
Unlike in Mackenzie's case, police and authorities have not said anything about any bodies being found.
Odero is also suspected of helping launder money for Mackenzie, according to court documents seen by Reuters in which police say "huge cash transactions" thought to be linked to the sale of houses belonging to Mackenzie's followers were traced to Odero's bank accounts.
Reuters could not immediately reach a lawyer representing Odero.