Detainees on Manus island have been raped and abused with the full knowledge of staff, a former senior guard at the Australian processing centre has claimed.

Speaking to SBS's dateline on Tuesday, the whistleblower alleged that repeated incidents of rape and assault occurred on the PNG regional processing centre and condemned the facilities as not even fit to "serve as a dog kennel".

Rod St George, the former G4S security senior manager on the island, claimed that assault victims were knowingly left in the same compound as their abusers as there are not adequate facilities to separate them.

"There was nothing that could be done for these young men who were considered vulnerable, which in many cases is just a euphemism for men who have been raped," he said.

Adding: "We might separate people in those circumstances on the mainland, but there aren't any facilities at Manus to do that, so these people who have been assaulted are forced to remain back in the tent."

The whistleblower also said that self harm and suicide attempts on the island were "very common – almost daily" . He said: "I've never seen human beings so destitute, so helpless and so hopeless before. I took the position with every intent of making the place a safer environment, but it proved quite rapidly to be an impossibility. In Australia the facility couldn't even serve as a dog kennel. The owners would be jailed."

He also claimed that a number of detainees had intimidated others into self-harming, and said that one detainee had been left injured after others had been "pouring solvents in his ear for some time".

The immigration minister Tony Burke confirmed on Wednesday morning that despite St George's allegations the government still plans to transfer asylum seekers to Manus under its draconian new "PNG solution" within a few weeks.

Burke, who is travelling to offshore detention facilities at Manus and Nauru on Wednesday, said he had had a "direct conversation" with the whistleblower and was starting to "work through these issues".

Speaking on ABC radio, Burke described the allegations as "horrific". He said that during his conversation with St George the whistleblower had made specific allegations, including that it was impossible to separate detainees if abuse allegations were made. He said he would be examining them directly.

He added: "He [St George] thought some of that may have actually been addressed since he left, but not sure whether it's been done to the full extent possible. I'll be in Manus for the next couple of days, and I'll have a look for myself."

The news comes as another boat carrying asylum seekers bound for Christmas Island sunk off the coast of Java on Tuesday night. The Australian Maritime Authority has said there were up to 100 people on board. Three deaths have been reported. The Indonesian search and rescue agency are mounting an operation in response.

Asked to comment on the allegations made by the whistleblower, a spokesman for Diac said: "The department takes all allegations of this nature seriously, and has initiated a process to obtain the full and specific details made Mr St George, so we can investigate his claims."

The spokesman continued: "The department is unaware of the claims on SBS dateline of "unreported acts of self harm" which are alleged to be "off the scale". Suicide attempts or incidents of self harm at the centre and any allegation of misconduct is taken seriously, and we encourage anybody with information about these allegations or other allegations to contact the department so we can investigate."

He said that the department was aware of one allegation of sexual assault in the Manus processing centre, but said the detainee did not press charges when interviewed by the PNG police. He said the department had seen no allegations of rape in the processing centre.

"Rape is a criminal offence in PNG. Any claim will be reported to police for investigation – transferees are encouraged to report personal safety concerns immediately," he said.