On Sunday afternoon, the Bishop of Townsville received an anonymous text message he’d spent nearly two decades waiting for: “Wheels up, the Bali 5 are on their way back to Australia”.

Timothy Harris, who provided pastoral care to the families of Scott Rush and Michael Czugaj after their arrest in 2005, immediately called Scott’s father, Lee. A short time later, they confirmed a plane carrying his son had landed in the Northern Territory.

“Their lost son has come home,” Harris said.

“Of course, they’re elated, but they know it is going to take a lot of effort to make sure the next part of Scott’s life is catered for with dignity and without a great deal of fuss.

“Every day of the last 20 years has been a nightmare for them.”

Rush, Czugaj, Matthew Norman, Si-Yi Chen and Martin Stephens have returned to Australia after the Indonesian government agreed to commute the rest of their life sentences for drug smuggling on humanitarian grounds.

A statement released on behalf of the five men and their families said they were “immensely grateful” to Indonesia’s president, Prabowo Subianto, and his government, as well as successive Australian foreign ministers who had advocated for their release.

The statement said the five men were “relieved and happy” to be back in Australia and that they looked forward to “reintegrating back into and contributing to society”.

But Harris said joining an Australian society they may no longer recognise would be very difficult.

“All sorts of things are going on at the moment in the Northern Territory, I know that much, to prepare them for what might come at them,” Harris said.

“Health is going to be an issue. The human body can only take so much. To be incarcerated like that for nearly 20 years has taken its toll.”

The prime minister, Anthony Albanese, confirmed the Australian government would support their “rehabilitation and reintegration”. The five men have been placed in temporary accommodation.

“After 19 years in Indonesian prison, it was time for them to come home,” Albanese said on Monday morning.

“I had the opportunity to speak to a number of the parents last night of these people. They are grateful that their sons have been able to return home.

“They did a serious crime and they have rightly paid a serious price for it. But it was time for them to come home.”

Harris said some of the men had formed personal relationships in Indonesia that would be difficult to leave. Matthew Norman and Martin Stephens have both married while in prison.

The terms of their repatriation state they cannot return to Indonesia. It is not known whether their spouses will be issued visas.

“Some of the hearts will be back in Indonesia,” Harris said. “I’m sure there is a bit of an [emotional] tug-of-war going on. There may be mixed feelings.”

The opposition leader, Peter Dutton, said he had spoken with the prime minister about the repatriation and did not repeat earlier criticisms of the deal made by some opposition MPs.

“These people don’t come back as heroes of our country,” Dutton said. “They haven’t been in political captivity. They have been sentenced under the rules of law that operate in that country for trying to import heroin.

“At a personal level and for their families, particularly coming into Christmas, you can understand the excitement and the relief that they’ll have.”

Indonesia’s senior minister for legal affairs, Yusril Ihza Mahendra, who struck the repatriation deal with Australia’s home affairs minister, Tony Burke, said the transfer was “reciprocal in nature”.

“If one day our government requests the transfer of Indonesian prisoners in Australia, the Australian government is also obliged to consider it,” he said in a statement.

But on Monday morning, when asked if there were “any payback arrangements expected” as part of the deal with Indonesia, Albanese said “no”.

The Bali Nine were charged and convicted with trying to smuggle 8.3kg of heroin out of Indonesia in April 2005.

The ringleaders of the drug-smuggling operation, Myuran Sukumaran and Andrew Chan, were sentenced to death and executed by firing squad in Indonesia in 2015. Another member, Tan Duc Than Nguyen, died of cancer in 2018.

The only female member of the group, Renae Lawrence, had her sentence commuted in 2018 and was returned to Australia.