Echiejile picked up a muscle tear during the friendly match against Greece and was replaced in the 23-man squad by Rangers winger Ejike Uzoenyi, who joined the team in Brazil on Wednesday.
“I am pained that Echiejile, who is a very key member of the squad will be missing out after putting in so much but there was nothing we could do to hasten the healing process,” Keshi said.
“We have spoken to the medical team and the NFF and we have agreed, so I was a bit shocked when I got a call from some of my friends back home that I insisted on an injured player.
“It’s a fallacy because I never spoke to anyone about Echejile.”
Nigeria will play their opening Group F game against Iran on June 16 in Curitiba.