The country's highest immigration official has contested allegations a five-year-old was raped on Nauru and lashed out at media reporting on the issue.

Key points: Department officials tell Senate estimates committee the alleged victim was actually over 10 years of age

Department officials tell Senate estimates committee the alleged victim was actually over 10 years of age Officials say the child suffered only "skin-to-skin" contact with another child detainee

Officials say the child suffered only "skin-to-skin" contact with another child detainee Department of Immigration and Border Protection secretary says "moral lecturing" unhelpful

The ABC last week reported the boy was facing the prospect of being returned to the offshore detention centre, where his attacker remained.

Paediatrician Karen Zwi said the young child suffered serious mental health problems after the alleged sexual assault.

Immigration Department officials today told a Senate estimates committee the alleged victim was actually over 10 years of age and the child suffered only "skin-to-skin" contact with another detainee child on the island.

Department of Immigration and Border Protection secretary Michael Pezzullo said media reports on the issue had been deeply misleading.

"It's getting to the point that there is advocacy parading as journalism that is actually deleterious to a sensible discussion about these matters," he said.

Mr Pezzullo also voiced cynicism in relation to claims of child sexual abuse in offshore detention, saying "in some cases, it's not what it seems".

The child in question could be sent back to Nauru alongside 267 asylum seekers in the wake of last week's High Court judgement, which upheld offshore immigration detention.

A number of state leaders have come out in support for the asylum seekers, calling on the Federal Government to grant amnesty.

But Mr Pezzullo today said "moral lecturing" was unhelpful.

He told Senate estimates the offshore processing system was working effectively and some asylum seekers could be ready for deportation "within days".

"No amount of moral lecturing by those who seem not to comprehend the negative consequences of an open-borders policy will bring forth solutions," he said.

"Yielding to emotional gestures in this area of public administration simply reduces the margin for discretionary action."

Federal Labor senators joined forces with Coalition politicians last week to vote down a Greens motion to grant amnesty to the asylum seekers in Australia, in contrast to calls for compassion from state Labor leaders.

Shorten stops short of backing calls to house asylum seekers

Victorian Premier Daniel Andrews and South Australian Premier Jay Weatherill have called on the Federal Government to allow the asylum seekers to remain in Australia, with both writing directly to Prime Minister Malcolm Turnbull.

ACT Chief Minister Andrew Barr has also pledged to take more asylum seekers during an exchange on social media.

Opposition Leader Bill Shorten said that he shared the frustration of his state counterparts, but emphasised the Coalition had "dropped the ball on processing people".

He told reporters last night that Federal Labor remained committed to regional processing.

"I believe that regional processing provides the best long-term sustainable solution," he said.

"But Malcolm Turnbull, if he doesn't want to resettle people here, he needs to do something about what's happening in Manus and Nauru."

Mr Turnbull has described the situation as "very delicate", saying yesterday that the transfer of the 267 asylum seekers would be looked at on a case-by-case basis.

He told the ABC there were "no policy options available in terms of border protection which are not tough which cannot be described as harsh".

Foreign Minister Julie Bishop declined to weigh in on the issue, saying it was up to the Prime Minister and Immigration Minister Peter Dutton to engage with the state leaders.

Update on 12,000-refugee intake from Syria, Iraq

The Senate estimates committee was also told today there were currently 295 people from Nauru in Australia, consisting of 15 refugees and 280 transferees.

There were 36 people from Papua New Guinea, including two refugees and 34 transferees.

Mr Pezzullo provided an update on the one-off resettlement of 12,000 people fleeing violence in Syria and Iraq.

He said 26 people had been resettled, more than 200 visas had been issued and more than 7,000 people had passed their initial assessment and were waiting on health and character tests.

The committee also heard costings for the rebranding of the Australian Border Force, totalling almost $10 million over 2014–15 and 2015–16.

New uniforms, which included protective items, accounted for $6.3 million while the cost of new envelopes totalled $10,000. Old stationery was destroyed at no cost.

The Senate estimates committee was also updated on the result of an amendment to section 501 of the Migration Act, which increased Immigration Minister Peter Dutton's power in terms of cancelling visas.

Mr Dutton had previously described it as providing for a "mandated arrangement for visas to be cancelled for people who had a conviction of 12 months or more imprisonment".

Since the amendment's introduction in late 2014, 36 New Zealanders stripped of their visas have successfully appealed the decision.

A total of 183 New Zealand citizens remain in onshore immigration detention, though only 174 had their visas cancelled on character grounds.

Editor's note (26/2/16): On 2 February ABC News reported that a five-year-old child being treated by paediatrician Dr Karen Zwi, had allegedly been raped on Nauru. The quotes attributed to Dr Zwi referring to a five-year-old were misattributed; Dr Zwi was referring to another case involving a 12-year-old boy. Dr Zwi has informed the ABC that her allegations do not include that a five-year-old was sexually assaulted.