Australia will recall its ambassador from Indonesia in response to reports of Andrew Chan and Myuran Sukumaran’s executions by firing squad.

Ambassador to Indonesia Paul Grigson will return to Australia on Friday for consultations.

His return is the endpoint of Foreign Minister Julie Bishop’s warnings that “there will be consequences” for the deaths of the two Australians who were caught in 2005 for organising an attempt to import heroin to Australia from Bali.

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• Indonesia executes Bali Nine pair Andrew Chan, Myuran Sukumaran

Ms Bishop said that Australia’s calls for a stay of execution “up to the very last minute” went unheeded.

“It is with a very heavy heart that I confirm, despite our ongoing efforts right up until the last minute to seek a stay of execution, our Australian citizens Mr Andrew Chan and Mr Myuran Sukumaran were put to death early this morning,” Ms Bishop said.

“Our concern centres on the fact that the apparent rehabilitation of Mr Chan and Mr Sukumaran was not taken into account. Rehabilitation is a fundamental aspect of a successful prison system.”

Ministerial contact between the neighbouring countries has been left as suspended, the Prime Minister Tony Abbott said. Once it was clear that executions for the pair were going ahead Australia suspended ministerial consultations between the two countries.

But while making strong statements that appear to reflect the distress felt for the families of the Bali Nine pair, Mr Abbott made comments which point to a more pragmatic, long term view of diplomatic relations.

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“It is important that this relationship, at every level, continues. I don’t want to personalise it but I do regret my representations which have been listened to patiently and courteously have not been heeded,” Mr Abbott said.

“My hope is that this presidency is a successful one, and while this is a dark moment in the relationship I am confident that the relationship will be restored for the great benefit of both our countries,” he said.

He said the executions were “cruel and unnecessary” because Chan and Sukumaran were “completely rehabilitated”.

The reformed drug importers Chan and Sukumaran were caught in August 2005 at Denpasar Airport having arranged for seven other Australians to carry heroin to Australia.

Their time in prison has been reforming, Chan became a priest and counseled other prisoners while Sukumaran became an artist.

Immediately following a press conference held in Canberra to announce the removal of Australia’s ambassador to Indonesia the coffins of the executed inmates emerged from Nusakambangan prison.