An official from the Department of Home Affairs who quit his job in the refugee processing area to argue publicly for an overhaul of Australia’s border protection regime has warned abandoning the medevac procedures would be “disastrous”.

Shaun Hanns, a home affairs departmental official until last October, has used a submission to a Senate inquiry into the medevac repeal to implore senators to persist with the current medical evacuations system as “the first step in an attempt to reform the system so that it is not only effective but as humane as possible whilst maintaining that effectiveness”.

Hanns said the medevac procedures actively demonstrate that Australia’s overall deterrence regime “need not rely on a logic of cruelty in order to be effective” – which is a break through in policy development in border protection that should not be lightly discarded.

“The experience of the past six months shows that there is significantly more leeway to change the system without undermining border protection than previously assumed,” Hanns said in a submission seen by Guardian Australia.

He has told the inquiry it is important to remember that people who have been transferred to Manus or Nauru are presently not eligible for any visa in Australia, and “anyone genuinely considered by the minister to be a risk to the community will, quite simply, never make it out of held detention”.

“Given the above, it’s entirely unclear how the current policy settings increase risk to the community in any way”.

The former independent Kerryn Phelps has also appealed to Senate kingmakers not to repeal the medevac procedures. She warns in her submission scrapping the current law will mean a return to the “slow, unpredictable and dangerous” transfer system for asylum seekers in need of urgent medical attention.

Phelps tells senators if they support the Morrison government’s efforts to dismantle the system, “the transfer of sick refugees will again be in the hands of politicians and bureaucrats, and we will return to the previous situation, when court orders and legal intervention were required to ensure critically sick people received the medical treatment they needed”.

The medevac procedures, which give clinicians a greater say in medical transfers of asylum seekers, were legislated in the last parliament with the support of crossbenchers, Labor and the Greens at the time Scott Morrison governed in minority. The change was opposed by the Coalition.

In her submission, Phelps argued crossbenchers pursued the overhaul because the “evidence was clear that an urgent medical solution was needed” and the medical transfer system was “broken”. She said 12 people have died in offshore processing, and it was clear when she assessed the expert evidence that the medical facilities on Manus Island and Nauru were inadequate for the needs of people in offshore detention.

She said a Queensland coronial inquest into the death of an asylum seeker in 2018 found the death was preventable, and was due to the failure of the Australian government to provide appropriate medical treatment and transfer to specialist care.

Prior to the medevac regime, Phelps said the only pathway for sick people to access urgent medical care was via legal intervention, which was “time-consuming and costly” and rarely successful for people on Manus Island.

“There was a real fear from doctors and other healthcare professionals that more people would die before they received appropriate medical treatment,” the former MP said in the submission.

“It was obvious that the only way to guarantee an appropriate and timely process, driven by clinical rather than political considerations, was through legislation.”

A separate submission from the Asylum Seeker Resource Centre said the medevac regime had enabled 110 people suffering from physical and mental health conditions to access urgent medical care in Australia.

“Prior to the passing of the medevac law, sick refugees were waiting an average of at least two years, and some for up to five years, for medical transfer after it had been recommended by the government’s appointed doctors, and the majority of transfers were the result of legal intervention,” the submission said.

It said in 2018, approximately 150 legal matters were run by over 100 pro bono lawyers, resulting in 50 applications filed, and the balance settled out of court.

“There have been 12 deaths in immigration detention offshore, many for treatable illnesses, and the medevac law ensures there is no longer political interference with the transfer system.”

The submission noted that in the majority of cases (around 80%), the minister had agreed in the first instance with the initial medical recommendation for transfer. “In only a handful of cases the independent health advisory panel has overturned the decision of the minister, and in the majority of cases has upheld the minister’s decision.” It said none of the cases refused for transfer under the medevac regime had been on security grounds.

The Morrison government has succeeded in getting the medevac repeal through the lower house, but the proposal cannot proceed to a vote in the Senate until later this year, because the repeal is subject to an inquiry by the Senate’s legal and constitutional affairs committee.

One of the key kingmakers in the Senate, the Centre Alliance crossbench senator Stirling Griff, has already put the Morrison government on notice that repealing the medical evacuations bill would “sully the relationship” between himself and the Coalition.

On current indications, the government will not succeed in repealing the regime unless the Tasmanian senator Jacqui Lambie supports the move. Lambie is yet to signal her disposition.

Phelps has appealed to Lambie to take her time and assess the expert evidence presented through the Senate inquiry. Phelps told Guardian Australia on Monday she spent many hours when she held the seat of Wentworth listening to experts working with asylum seekers and medical practitioners, “and it didn’t take long to discover a catastrophic situation had been created”.

The independent health advisory panel overseeing medevac procedures has reported there were 73 admissions covering 43 people at the RPC medical centre on Nauru in the first quarter of 2019, with “the majority” relating to mental health conditions.

The first quarterly report of the independent panel, obtained by Labor under an order for the production of documents in the Senate, found that in addition to the 73 admissions, with stays ranging between one and 44 days, there were 8,260 medical consultations provided to people on Nauru in the quarter – mostly for mental health problems.