Amnesty International declared its claims as "damning", and labelled Australia's maritime border control policies as a "lawless venture".
The advocacy group has released a report called ‘By Hook or By Crook’, a phrase coined by former prime minister Tony Abbott to describe Operation Sovereign Borders.
It refers to two key dates in its findings.
In May, Amnesty claims more than $40,000 was handed over to crew members intercepted on a boat on its way to New Zealand.
It says that money was paid to get the crew to return to Indonesia instead.
Anna Shea, who wrote the report, said her research was comprehensive.
"I spoke with everyone who had been on board that boat,” Ms Shea told SBS World News.
“They said the crew had received money. The crew told me that they had received money. Indonesian police told me that they found money on the crew, and they showed me the money.
“This is all very serious and compelling evidence. The asylum seekers told me that they were held on a border force ship in very crowded, hot, airless cells. They were locked inside. They were denied access to medical treatment."
The Indonesian government has previously stated it believes Australia had paid the ship's crew during that operation.
Meanwhile in July, Amnesty alleges Australian officials intercepted a boat and separated the two Indonesian crew and 15 passengers on a Border Force ship for a week.
Ms Shea said there are questions whether money was also exchanged during that encounter.
"We don't have the same level of proof as we did for the May incident but asylum seekers told me that after they were transferred onto a new boat by Australian officials,” Ms Shea said.
“They said the crew members had bags that they didn't have before and that Australian officials seemed very, very worried about anybody touching these Amnesty International has called for a Royal Commission into the federal government's border protection policies, but Immigration Minister Peter Dutton has rejected the findings, calling Amnesty a "disgrace".bags, but we can’t say for sure.”
Report rejected
Immigration Minister Peter Dutton has denied the allegations, saying people are lawfully intercepted at sea under safe conditions.
Speaking on Radio 2GB, he accused Amnesty of casting a slur on border officials.
"They don't like Operation Sovereign Borders, they try and attack the border force staff and the naval staff and I think it's a disgrace,” Mr Dutton said.
“I think in the end you can take the word of the people smugglers or you can take the word of our staff at Australian border force, and people will make their own judgements."
Foreign Minister Julie Bishop has also rejected the report.
“Australian officials are acting in accordance with Australian domestic law and in accordance with Australia's international obligations,” she said.
It comes as a Senate inquiry continues to investigate the May operation, but Amnesty believes that is not enough.
Ms Shea said the group wants a Royal Commission to determine whether border and maritime officials engaged in criminal activity.
"The Royal Commission can do things like recommend criminal charges and make policy recommendations, but a Senate inquiry has a narrower scope of powers so that's why we're asking for a Royal Commission,” she said.
“This is a serious thing for Amnesty to ask for, this is not something that we do lightly and it's not something that we've done before. We're very worried about what our research has uncovered and that's why we're asking to get to the bottom of it."
‘A horrible experience’
Former Salvation Army employee Mark Isaacs spent several weeks on Nauru in 2012, to provide support for detainees.
He said he has seen asylum seekers mentally break down as a result of their time in the centres.
"Pretty much when we arrived there it was a pretty horrible experience,” he told SBS World News.
“We saw all sorts of acts of self-harm, of suicide attempts. I also saw men lose their minds and have mental breakdowns."
Mr Isaacs believes the treatment of asylum seekers is extremely poor.
"In terms of working there it was the attitudes which were worrying for me, the attitude that many people thought that the system of abuse was justifiable," he said.
Mark Isaacs’ father, David Isaac, is a paediatrician and also spent some time in Nauru last December caring for children there.
He said what he saw left him shaken.
"I've never seen anything so traumatic in all my life as the children I met there,” Mr Isaacs said.
“Just the level of distress in the parents, in the children, in every child I saw, was just awful. And on average they had been there 14 months without knowing what was going to happen to them."
Future of asylum?
Activist groups have lobbied the government to shut down its detention centres, as well as improve its standards at sea.
Minister Dutton was again dismissive of such suggestions.
"People need to understand this message, including the refugee advocates here. We are not going to water down our policy when it comes to boats. We are not going to allow people to settle in Australia if they've sought to come here by bought,” he said.
“We've been clear about it, we've been consistent about it, we're not going to take a backwards step and we're not going to be bullied into some watering down of that."
Mark Isaacs believes if detaining asylum seekers must continue, an open dialogue with the public is essential.
"I think we need open and transparent systems of detention, if we are going to have detention centres,” he said.
“I think we need to allow media to report on detention centres we need the Australian public to be able to see what's going on inside the centres. I think we need to change the conversation to refer to these people as 'people' - to treat these people as people."
