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Lisa Wilkinson has accused Christopher Pyne of defending the Indonesian government's highly militarised treatment of two Australians facing the death penalty.
On Friday's edition of the Today show, Wilkinson grilled the education minister about why he was excusing Indonesia's use of armoured police vehicle and riot police to move Andrew Chan and Myuran Sukamaran.
She also raised the issue about photographs of a beaming police commissioner standing next to the condemned men on their flight to the island where they will be executed.
"He's (President Joko Widodo) treating these men like prime catches, and thumbing his nose at us," Wilkinson said.
When Mr Pyne said Indonesia was treating the two Australians no differently to other foreign prisoners in the same situation, Wilkinson disagreed.
"No that's not true Christopher because one of the other drug smugglers left in an unmarked van to go the same island facing the same fate," Wilkinson said.
"But you're apologising for him, with the greatest respect."
The federal government will make a formal complaint to the Indonesian government about the "lack of dignity" shown to the pair.
Mr Pyne denied he was apologising for the Indonesian government and said he was completely opposed to the death penalty.
"The Australian government's response which so far has been a model of maturity and totally supported by the opposition in a very bipartisan way has been to be calm and to be sensible. It certainly hasn't been to try and pour oil on the fire," Mr Pyne said.
"We certainly don't want to get into a fight with the Indonesians which causes them to get their backs up. We will not be able to save these two men's lives by insulting President Widodo or the Indonesians."
Wilkinson also asked about clarification about the consequences the Indonesian government will face if they proceed with the execution. Both Mr Pyne and shadow minister for infrastructure Anthony Albanese reframed the question.
The interrogative approach to federal leaders is another step in the increasingly outspoken journalist's approach.
Just last month, Wilkinson told Fairfax Media she owed it to her audiences to not go gently on political guests.
"There is nowhere a politician [can] get in front of more everyday Australians than breakfast television," Wilkinson said.
"Our audience don't want us to beat up politicians on the show but they also don't want us to go softly, softly on them either."