In some instances, girls have suffered prolonged bleeding for as long as 12 months, weight gain of up to 20kg, hair loss and migraines.
In more severe cases, there were reports of internal bleeding, anaemia and depression.
But medical professionals still claim Implanon is one of the most effective methods of contraception.
The implant works by emitting a synthetic hormone called progesterone via a small rod that is surgically inserted into the upper arm.
Monash University drug discovery biology senior lecturer Sabatino Ventura said Implanon stopped ovulation.
“The Implanon thickens the cervical mucous to stop the progression of sperm through the reproductive tract and affects the lining of the uterus which can inhibit implantation of a fertilised egg, too,” he said.
“The manufacturers claim it is 99.9% effective.”
An implant is designed to last three years and is much less popular than the oral contraceptive.
Many girls who have had the Implanon said they had decided to have it removed.
Stephanie Tartagalia, 18, said her mother was a nurse and had told her it was the best method of contraception.
Amy Dangerfield, 18, said she had Implanon implanted in February but had it removed five months later.
“When it was inserted, my whole upper arm was purple for two weeks,” Amy said.
“My hair was falling out in chunks, my mood was out of control all the time and I was constantly bleeding with headaches all the time.
“The doctor chose to remove it for safety reasons and I won’t ever get it again.”
Mr Ventura said such side effects usually disappeared after a few months.
“Some women will have more severe effects and may need to stop treatment and use another contraceptive method,” he said.
Sexual Health Quarters director of information and education Rebecca Smith said Implanon and other long-lasting reversible contraceptive methods were usually the most effective.
“Anecdotally, the negatives seem to be reported on in the media a lot more than all the positives,” she said.
“Those people [who suffer from severe side effects] are in the minority.”