Samson Mwathethe has said reports suggest al Shabaab militants in Somalia are using some KDF soldiers as human shields.
This brings to the fore al Shabaab's earlier claim that it captured soldiers in an attack on an African Union base in Somalia on Friday.
The group, which did not give the number of soldiers being held, also said in a statement that more than 100soldiers were killed, revising up the number from 63.
Some websites in the country reported that the al Qaeda-linked militants captured 12 soldiers in the attack in El Adde.
Mwathethe, who is the Chief of Defence Forces, noted that the information demonstrates how delicate a search, rescue and recovery operation operation is.
But he added that "the enemy has been degraded" and that security forces will not let Kenya suffer more casualties.
In a statement on Sunday, Mwathethe noted the public's need for details on the assault but said the operation was the priority at this time.
"Al Shabaab are evolving and competing for space but this does not undermine our operational and combat capability," he said.
"Our resolve to combat terrorism remains," he further said, and noted that Kenyan forces closed in on the militants in a "concerted effort of land air assets".
The Chief of Defence Forces asked the public not to share information that could compromise Kenyan troops' pursuit of the terrorists. He said updates will be released as they become available.
Mwathethe commended soldiers killed in the ambush which has been described as the deadliest since KDF joined the African Union Mission in Somalia in 2011.
To their families he said: "I assure you that the Kenya Defence Forces will stand with you till the end.."
"The blood of our fallen heroes was not shed in vain. We will fight them [al Shabaab] deep in their hideouts. We will smoke them out of their caves and follow them to the end in honour of every drop of blood of Kenyans."
Early Sunday, several Kenyan soldiers injured in the attack were flown to the country. Four were received at Wilson Airport in Nairobi following the attack whose number of casualties is yet to be released.
In a statement at the airport on Sunday, Defence CS Raychelle Omamo said the attack was launched against a company-size force of soldiers, without making clear if this was the size of the Kenyan contingent in the area or the mixed force.
A military company can range between 80 to 250 soldiers. Al Shabaab often cites higher figures for death tolls than those given by officials, who usually play down the numbers.
Details will be sent directly to families, Omamo said, adding: "Allow the families privacy as they mourn. Full details of those injured and killed will be made public after families affected are notified."
"The soldiers who were airlifted were critically injured. Be patient, information will be availed to you. We are determined to bring our soldiers home," she also said.
Amisom has driven al Shabaab from major strongholds in Somalia in a wave of offensives. But the group still controls some rural areas and frequently launches attacks saying it wants to drive out the "invaders".
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