Hajah Noraihan, the Malaysian consul to Uganda, said despite an early warning to the Ministry of Foreign Affairs in 2008 when the number of trafficked girls stood at 30, the constant flow of victims has not slowed.
She says Malaysian intelligence indicates 10 girls continue to fall through the cracks of Uganda's immigration and labour systems daily.
"Nothing was done and this is what happened," Ms Noraihan said.
Malaysia, a country known for its poor human trafficking record although it has traditionally been within the Asian region, is currently on a US state department watch list for not having shown adequate evidence of its efforts to combat the scourge.
However, it has been working to curb the illegal practice after a raid last October in which 21 Ugandan girls were freed from forced prostitution.
Only five of these have since returned to Uganda, while the rest are being held in a Malaysian detention centre, Ms Noraihan said.
A total of 60 girls are being held on fraudulent visa charges as a result of an ongoing immigration sweep.
The line between girls who are "caught" or "saved" as Ms Noraihan terms them, is often a matter of technicality. A victim's silence or shame can see them face criminal charges instead of being brought back to Uganda, she said.
The International Organisation of Migration (IOM) says it has successfully returned 14 girls to Uganda from Malaysia, but that they are only able to move victims who have been clearly identified and volunteer to come home.
Director of Interpol Asan Kasingye, who confirmed the figure of more than 600, said young, poor and vulnerable girls are targeted by recruiters after being lured overseas with the promise of legitimate high-paying jobs.
He said many more may be trapped in an unknown location, or are intimidated into silence by their captors.
According to Ms Noraihan, three Ugandan women have been killed in Malaysia since 2010 for trying to escape.
Mr James Mugume, the permanent secretary of the Ministry of Foreign Affairs, said he was unaware of the staggering figures the consul presented. However, he said an Internal Affairs committee made up of Interpol, Immigration and Ministry of Labour representatives has been tasked with identifying recruiters and addressing lax immigration procedures.
The return trips for the 60 girls still in Malaysian prisons will have to be funded by their families or the IOM, Mr Mugume said.
"The biggest issue is we have to stop the traffic from here," Mr Mugume said. "You have to focus on the root causes - who is recruiting these people?"
Mr Kasingye said he could not discuss the details of the case, but that "some" people have been arrested and charged in Uganda.
He added that it has been difficult to bring suspects to justice with so few witnesses available in the country, as most are still in Malaysia.
However, Mr Kasingye said the findings of an ongoing investigation into a number of registered security companies suspected of involvement in fraudulent employment practices will be presented before Parliament this month.