The CS was responding to a statement posted by lawyer Miguna Miguna, who castigated reports that Murkomen had formed the said team.
"As a department of transport, we don’t investigate military planes. Our work is strictly restricted to civilian airplanes," Murkomen responded to Miguna.
In his post, Miguna had laughed off the claims made by a section of leaders that the CS had formed a team, saying only the President of Kenya has the powers to form such a team and gazette it.
Miguna said the position of the Chief of Defence Forces is higher in rank compared to that of the deputy president and the Cabinet Secretary, and therefore it was not right that people were talking of a team formed by the CS.
"Remember that no one except the President of the Republic has the mandate to set up a team investigating the death of Kenya’s Chief of Defence Staff. Not a cabinet secretary," Miguna said.
"Moreover, the military will not cooperate with that purely civilian team, honour its summons and comply with any directives from or findings by it. We must be a country that adheres to the rule of law and avoids the tendency of engaging in PR exercises on such grave matters," Miguna added.
General Ogolla died in a military chopper crash in Elgeyo Marakwet on Thursday while on official duty.
Nine other soldiers also perished in the crash, with only two surviving.
Ogolla was laid to rest on Sunday at his rural home in Alego-Usonga, Siaya county, in a ceremony attended by President William Ruto and other high ranking officials in the government and military.
Ruto promised to get to the bottom of the crash and said he will ensure the findings of the investigations are made public once they are complete.