In a submission to a Senate inquiry examining the government's bid to unwind the laws, Dr Phelps points out that about 80 per cent of cases were agreed to by the minister at the first instance and none have been refused on security grounds.
"The process is working as intended - an orderly system providing medical treatment for sick refugees in a timely manner," Dr Phelps said.
An independent health panel has overruled the minister eight times, allowing allow transfers to proceed.
The government used its majority in the House of Representatives to pass the repeal legislation but still requires the vote of key crossbench senators.
If the original bill is overturned, Dr Phelps warned critically ill people will again be in the hands of politicians and bureaucrats.
"We will return to the previous situation when court order and legal intervention were required to ensure critically sick people received the medical treatment they needed," she said in the submission released on Monday.
"Doctors will again fear further unnecessary deaths and a return to a slow, unpredictable and dangerous transfer system."
The fate of the medevac legislation lies with Senator Jacqui Lambie, who is yet to reveal her position.
Dr Phelps has met with the Tasmanian independent since her re-election in May and on Monday requested another meeting with her.
"My key message to her is that the medevac legislation is saving lives," Dr Phelps told SBS News on Monday.
In a separate submission, the Asylum Seeker Resource Centre said prior to the Medevac law sick refugees were forced to wait an average of at least two years for medical transfer even after doctors had made the recommendation.
Some waited up to five years.
"The medical transfer system was failing sick people, there were 12 deaths offshore and transfer requests were routinely delayed or ignored," the ASRC submission stated.
"The only way to guarantee an independent, robust and orderly medically led process is to retain the Medevac Law."
"There are still sick refugees in Papua New Guinea and Nauru who require a timely doctor-led process to assess their medical needs and transfer requests."