Rajapaksa is arriving today in Australia to participate in the CHOGM to be held at Perth.
Jegan Waran, a retired engineer who migrated to Australia from Sri Lanka, said before the Magistrate that he witnessed and was still haunted by what he saw in the hospitals and displaced persons camp at the end of civil war.
Waran, who returned to Sri Lanka in 2007 to volunteer in Tamil hospitals, schools and displaced persons camps, alleged that Sri Lankan forces had deliberately attacked clearly-marked civilian infrastructure such as hospitals and camps.
"Everybody who's alive today, it's a miracle that they have escaped death or injury," Waran was quoted by ABC today.
Waran is an ethnic Tamil and sympathised with the Tamil Tigers or LTTE, which fought for a Tamil nation for decades until their defeat in 2009 by Sri Lanka's military forces.
"Patients who were in the hospital were killed, and there were other patients waiting for treatment, they were killed. There was a medical store where they kept the medicines; those were destroyed, scattered all over the place, you can see. Ambulances were destroyed. So I have seen that personally," Waran said.
Waran, now an Australian citizen, said that on Christmas Day of 2008, drones circled another hospital before Sri Lankan Air Force planes attacked.
"The hospital, clearly a big Red Cross sign was marked on the roof, and drones usually take surveillance, so I am very positive that they know where the hospital is and they know it will be damaged," he said.
This and other incidents have led him to issue summons for three war crimes charges against Sri Lankan president.
He said, he wanted to bring these charges against the president "because I feel that he's the commander-in-chief and nothing would have happened without his knowledge or his directions, and ultimately, he should be answerable to what was happening".
However, Sri Lankan government has repeatedly denied allegations of war crimes.
Though accusations against Sri Lankan armed forces deliberately attacked civilians are not new, but its the first time charges have been brought by an Australian citizen in an Australian court.
The federal Attorney-General Robert McClelland will need to give final approval for the Australian indictments to proceed.
Lawyers in the case have asked federal Attorney-General to become involved, but a spokesman for McClelland said the Attorney-General has not been informed of any criminal matter or charges relating to Rajapaksa.
"We have written to the commissioner of the AFP and we have written to the Commonwealth Attorney saying here's your opportunity, Rajapaksa will be in Australia, it's appropriate to conduct those investigations," Waran's lawyer, Rob Stary said.
Last week, Victoria's chief magistrate authorised the charges brought by Waran to proceed, noting that they satisfied Victoria's Criminal Procedure Act.
"These are not frivolous or vexatious complaints; they are bona fide credible complaints," Stary said.
ABC report said the Sri Lankan government refused to offer of an on-camera interview but issued a statement.
"The issue of the proceedings which are apparently to be the subject of your story are plainly a violation of Australia's obligations under public international law," the statement said.
Furthermore, the purported proceedings are incompetent under Australian law.
Australian Prime Minister Julia Gillard has said that the war crimes case filed against the Sri Lankan president cannot proceed without the federal government's consent.
"No such legal action can be taken on an issue like this without the consent of the attorney-general," Gillard was quoted as saying by Australian news agency AAP.
"And the attorney-general hasn't received any request in relation to this matter," she said.
She said her government was concerned about the persistent war crimes allegations.
"Australia and like-minded countries have been urging and will continue to urge Sri Lanka to address the serious allegations that have been made of human rights violations," she said.
The indictment was filed under the Australian criminal code and is now set for hearing on November 29