MAAU president Datuk Seri Shahidan Kassim said the trio underwent the doping test on June 23 and waiting for the results.
The three athletes - Norjannah Hafizah Jamaluddin, Nurul Sarah Kadir and Noor Imran Hadi - had gone missing when the NSI requested them to undergo a medical and dope test in Bukit Jalil on May 24.
However, two days later, they were reported to have left to Bulgaria for a training stint.
"Apart from undergoing dope tests, they have also participated in a few competitions," said Shahidan when met by reporters after the KL International Marathon here Sunday.
"They will return to Malaysia next month and prepare for the Asian Athletics Championships in Kobe, Japan from July 7-10.
NSI Director-General, Datuk Dr Ramlan Abd Aziz had said that NSI would seek the assistance of the Regional Anti-Doping Organisation (RADO) in Europe to conduct the tests.
"If an athlete was found positive, it would be up to MAAU to mete out the appropriate punishment by setting up a panel as a normal procedure.