Pictures published by local media show Ms Leifer about to board a flight surrounded by people wearing personal protective gear including masks and face shields.
She is expected to arrive later on Monday.
One of her alleged victims, Dassi Erlich, also tweeted on Monday that "Leifer is on the way back to Australia".
Ms Leifer is wanted in Australia on 74 charges of child rape and sexual abuse stemming from her time as principal at Melbourne's Orthodox Addas Israel School.
Mr Waks said it was unclear how long Ms Leifer's case would take to progress through Victoria's legal system given COVID-19 delays.
"We expect that Leifer's return to Australia will impact many people," he said in a statement.
"VoiCSA remains committed to helping anyone who may have been sexually abused by Leifer."
"The first point of interest will be to see who is appointed to represent Leifer. Will her supporters continue to raise enormous sums of money towards her defence and will some of those funds come from the Adass Israel community in Melbourne? Alternatively, will she rely on a public defender that will be offered to her?" Mr Waks asked.
Israel's Supreme Court approved her extradition order in December and Justice Minister Avi Nissenkorn approved the order the following day.
Her final failed appeal followed 74 hearings in Israeli courts, which have been drawn out on the basis of Ms Leifer claiming mental illness.
Ms Leifer fled Australia to Israel in 2008 when the allegations arose, using a plane ticket allegedly paid for by the Addas School.
Ms Leifer was first arrested in Israel in 2014 and placed under house arrest, only to be let free again on the condition she undertook psychiatric assessments.
Following an independent undercover investigation that proved she was feigning mental illness and going about her life as normal, Ms Leifer was arrested again in 2018.
Readers seeking support can contact Lifeline crisis support on 13 11 14, Suicide Call Back Service on 1300 659 467 and Kids Helpline on 1800 55 1800 (for young people aged 5 to 25). More information is available at BeyondBlue.org.au and lifeline.org.au.
Anyone seeking information or support relating to sexual abuse can contact Bravehearts on 1800 272 831 or Blue Knot on 1300 657 380.