The drug resistant strain of the parasite was first discovered in the border areas of western Cambodia in 2005, but has now spread right through Southeast Asia towards India.
Professor Nicholas White from the Bangkok-based Mahindol Oxford Tropical Medicine Research Unit has called on governments and the World Health Organisation to take a tough approach, but says he's concerned there isn't the political will.
"Here we have a fire breaking out which could imperil everyone in the tropics and literally kill millions of people," he said.
By 2007, the research unit was convinced the parasite was entrenched in Cambodia's western region, but they didn't realise it had already spread beyond the country's borders.
Seven years later, the deadly drug-resistant parasite is not just firmly established in Cambodia but in Thailand, Vietnam and Myanmar, and is knocking on the door of India, Bangladesh and Laos.
"Resistance has emerged from the southeast Asian region, not once, but twice before [and] marched across Asia and killed millions in Africa," Professor White said.
"That is a potentially looming emergency."
He says the growing prevalence of the drug-resistant parasite is a huge blow to the fight against malaria and could reverse all the progress made in the last decade.
During this time malaria deaths have fallen by a third, and three million lives have been saved.
"The main reason has been these drugs, the artemisinin combination treatments, and getting them out to the people who need them has had an enormous effect," he said.
"So malaria has been improving and we've even begun to re-entertain the idea of eliminating malaria."
'Urgent action needed'
Professor White now says he's not even sure this crisis can be contained.
"In those areas, lots of people are walking around - apparently healthy - carrying the malaria parasite."
"We think you probably have to treat everybody in those areas.
"That's called mass drug administration and it's controversial."
Professor White says he's not convinced governments are willing to take the steps needed to deal with the issue.
"There's endless meetings and much ringing of hands and expressions of concern, but translating that into the radical, dynamic and tough action - which will be outside the health sector, a lot of it - I'm not sure there is the appetite for that yet," he said.
He says its a stark contrast to the global response to the Ebola outbreak.
"The Ebola virus - now there's a nasty infection that might kill you and me, we take that very seriously," he said.
"The problem with malaria is that it mainly affects poor, disenfranchised people living in remote rural areas, and they don't have such a loud political voice."
Researchers share concern
Other malaria researchers are also concerned about the lack of action.
Dr Rowena Martin, a leading researcher of malaria drug resistance at the Australian National University's Research School of Biology, agrees that swift action is vital.
"This has happened before, this is the same region of the world that brought us chloroquine resistant malaria parasites and parasites resistant to other types of anti-malarial drugs," she said.
This time around, malaria research teams are doing everything they can to contain the drug-resistant strain.
Dr Freya Fowkes, the head of malaria epidemiology at the Burnet Institute in Melbourne, has been collaborating with Professor White's team in Thailand.
She says current research is focusing on trying to contain and eliminate the drug-resistant parasite within southeast Asia.
"Artemisimin currently treats 300 million people every year with malaria, so if we lose this drug ... what are we going to treat those 300 million people with? It really is crucial that we stop drug resistance."
However that's easier said than done.
Dr Martin says it's almost inevitable that all anti-malarial drugs will eventually lose their effectiveness.
She says another strategy is pairing drugs together in combination therapies - as the parasite acquires resistance to one anti-malarial drug it becomes hypersensitive to another.
This type of treatment could slow down the parasite's ability to develop resistance.