"It was not part of our schedule," Mills said.
Mills said Bolt had known for several months that he would not be going to the Commonwealth Games.
"The time would be when he would be doing his background training for next year's world championships," he said.
Bolt has always said he would defer to his coach on whether he would compete in the Games.
The world 100 and 200 metres record holder will also miss next weekend's national championships.
"He was never down to run the (Jamaican) trials," Mills said.
The world's fastest man resumed track training on Tuesday after being sidelined for several weeks with a sore Achilles tendon.
"He has not started any extensive work but he is all right," Bolt's long-time coach said.
Bolt's next scheduled race is a 200 metres at the Lausanne Diamond League meeting on July 8.
"That is the schedule, but we will see how it goes," Mills said without elaborating.