Young-looking children were chosen to be transferred to the harsh Manus Island refugee detention centre to discourage other refugees from coming to Australia, an inquiry has heard.

And children detained in facilities on Nauru are suffering illnesses and mental conditions caused by unsanitary and inhospitable conditions on the island nation while all refugees are subjected to a broad "intention to dehumanise".

Former officials, charity workers and doctors who worked in the immigration system have given at times distressing evidence to an Australian Human Rights Commission (AHRC) inquiry into the fate of children caught in Australia's detention centres.

Gregory Lake, the former director of offshore processing and transfers at the Department of Immigration and Border Protection, told the inquiry he was directed by a ministerial staff member to choose the youngest-looking children from among those eligible for the first transfer of detained people from Australia to Manus Island in 2012, when Labor was in government.

"Because they wanted to send a deterrent message, it was important to send some children, to say that children are not exempt from transfer," Mr Lake said.

"The first time children were sent to Manus or Nauru, I received a phone call from the minister's office and one of the staff members asked me if the family groups selected ... included any young children."

Criteria for transfer included a Papua New Guinea government requirement that children be inoculated against Japanese encephalitis - something that could not be done to children under seven years of age.

This was not publicised, Mr Lake said, because of fears smugglers would put children under seven on boats to avoid offshore detention.

Mr Lake said he had a list of families with children aged seven to nine.

"My responsibility according to this phone call was to select the children that looked the youngest," he said.

Mr Lake resigned from his role as director of processing and transfers at Nauru in April 2013.

He told the inquiry the language used in the detention centres - such as calling people "clients" and referring to them by identification numbers rather than names - had a dehumanising effect on asylum seeks.

"The language is not a strategy in and of itself but it is definitely part of a broader intention to dehumanise," he said.

"The way that immigration detention centres are run, particularly now under a deterrent framework, is designed to construct an environment where people are used as examples to say `you're subject to this - it's going to be worse for you to be in Australia than it as to be where you came from'."

The inquiry also heard from Australian GP Ai-Lene Chan, who worked at the Nauru and Christmas Island detention centres in 2013 and 2014.

Dr Chan told the inquiry that children on Nauru were suffering from bacterial skin infections, conjunctivitis and ear infections that would be easily treated in Australia with basic sanitation, but became chronic and debilitating in the harsh conditions of the centre.

Dr Chan also said she examined many people who were suffering dehydration because water was not available throughout the day, and because some women and children wanted to avoid the unclean toilet facilities.

Temperatures on Nauru could exceed 40C, she said.