Professor Triggs said there was also evidence children had swallowed detergents or other poisons, put plastic bags over their heads, cut themselves and used the hijab to try to hang themselves.
"The head-banging is very common," she told the ABC's 7:30 program.
She said Mr Morrison needed better advice if he doubted the evidence.
"I'm afraid I believe that the minister needs to be better advised."
Professor Triggs said all children should be removed from the detention centres and placed in the community.
She also said Mr Morrison's statement that children in detention received daily care was not true.
"It doesn't appear to be true on the evidence that we're receiving," she said.
The poor health of children on Christmas Island would be unacceptable if it were found in a Sydney suburb, Professor Triggs said.
"There were children with big lumps, untreated sores, red eyes.
"But most of them were coughing, had asthmatic conditions or stomach complaints. You would not tolerate that as a neighbour, as somebody meeting another person in a school environment.
"There, it's endemic."
Professor Gillian Triggs should be commended strongly for her efforts. As I heard the report, it became obvious that a single locale is needed for unscheduled refugee arrivals. We need to put substantial financial resources into Nauru to make it a proper stopping place for everyone. Christmas Island and the onshore detention centres are creating a division of labour that is difficult to supervise and is proving unsustainable. The protection of all the persons affected by our laws should be the first concern. There are fewer and fewer unscheduled arrivals. Putting the necessary resources into a first class offshore centre may cost more, but it will result in improved care for everyone and a far better relationship with the people of Nauru. Simultaneously, we need to open our doors much more widely to refugees in overseas camps. Currently, “legal” (as opposed to what the government terms “illegal”) refugee resettlement is a mere trickle.