The Immigration Department has contradicted its earlier version of what happened during a shooting on Manus Island on Good Friday, revealing that nine people were injured as "many" shots were fired into the refugee compound by PNG defence force personnel.

Key points: Immigration Department Secretary Mike Pezzullo says "quite a number of shots" were fired into the compound

Immigration Department Secretary Mike Pezzullo says "quite a number of shots" were fired into the compound An earlier statement originally said only one weapon was fired and no-one was injured

An earlier statement originally said only one weapon was fired and no-one was injured Mr Pezzullo stressed to Senate estimates that the original statement was based on the information available at the time

A statement from the department originally said a weapon was fired into the air and no-one was injured.

But department secretary Mike Pezzullo corrected that today, telling a Senate Estimates hearing "it appears that the number of weapons deployed was greater than one".

"Some shots — quite a number it seems — were fired laterally into the compound," he said.

"Many more shots were fired.

"It was an unacceptable — from our point of view — breakdown in the discipline of the relevant personnel who went to their accommodation accessed those weapons and fired those rounds."

He stressed to the committee that the original statement was based on the information available at the time.

Border Force Assistant Commissioner Kingsley Woodford-Smith told the Senate committee nine people were injured, none seriously.

He said five were service providers, one was a PNG Defence Force Officer, another was employed by the Immigration Department and two were asylum seekers living in the compound.

In April, Immigration Minister Peter Dutton told Sky News the Good Friday shooting was sparked because locals were angry after asylum seekers allegedly led a local boy towards the centre.

"I think it's fair to say the mood had elevated quite quickly. I think some of the local residents were quite angry about this particular incident and another alleged sexual assault," he said at the time.

PNG Police Commissioner David Yapu said a 10-year-old boy was given fruit by residents of the processing centre, but said nothing happened to him and no official complaint had been made.

Border Force Commissioner Roman Quadvlieg today told the committee of rising tensions and a febrile environment on Manus Island, and said anything could spark "something like the Good Friday incident".

He listed a series of incidents in the Lorengau township including "bartering and exchange of money and goods for sex with the local women by the RPC [regional processing centre] residents".

Roman Quadvlieg told the estimates hearing of rising tensions on Manus Island. ( ABC News: Marco Catalano )

Mr Quadvlieg also said a resident of the processing centre had been charged with a number of counts of sexual penetration of a child after an incident in March this year.

And despite Commissioner Yapu's view, Mr Quadvlieg said a child under 10 was taken into the centre.

"The very fact that a child under the age of 10 is in an environment where there are single adult males — after dark — and that child is left unattended even for minutes at a time is of fundamental and profound concern," he said.

"When you take that incident as I have just described it and you insert that against the backdrop of the broader environment and landscape that I have described, it is in my operational experience almost inconceivable to assert there is no correlation between that incident and rising tensions on the island," Mr Quadvlieg said.