Mr Abbott defended commissioner Dyson Heydon a day after the former High Court justice questioned Opposition Leader Bill Shorten's credibility as a witness.
Mr Shorten spent two days on the stand at the commission, being quizzed over his days as the Victorian and national secretary of the Australian Workers Union.
The commission discovered Mr Shorten only declared on Monday a $40,000 campaign donation that labour-hire company Unibilt made in 2007.
Following the revelation, former ALP national secretary Bob Hogg called for Mr Shorten's resignation.
But Labor frontbencher Anthony Albanese said Mr Shorten's time at the party's helm was certainly not over, having given "vigorous testimony".
"He answered every question that they had and he did it in a way that was forceful and defended his record that he is proud of," Mr Albanese told Channel Nine on Friday.
Mr Abbott declined to offer any advice on Mr Shorten's future.
"Obviously the royal commission has exposed the underbelly, if you like, of dodgy unionism in this country," Mr Abbott told reporters on the Gold Coast on Friday.
"I'm not in the business of giving public advice to other political parties."
He again called on Labor to pass two pieces of legislation that crack down on unions.
"If the Labor Party wants to get its act together, wants to ensure that we never have this kind of problem again, it should get cracking and help the government to pass this legislation," he said.
Commissioner Heydon warned Mr Shorten on Thursday against giving "non-responsive" and lengthy answers and said he was concerned about the Labor leader's credibility as a witness.
Mr Abbott said there was no more distinguished person in the legal profession than Justice Heydon.
"He is conducting this royal commission in accordance with the usual canons of fairness and exactitude and he is doing exactly what royal commissioners should do," the prime minister said.
But opposition MPs are accusing the Abbott government of staging a political witchhunt.
Labor frontbencher Brendan O'Connor told ABC radio it was a conflict of interest for Mr Abbott to spend $80 million of taxpayer money to go after his political opponents.
Labor senator Sam Dastyari labelled the coalition-established royal commission an "Americanisation of Australian politics".
However, the ABC reports MPs are privately conceding Mr Shorten has lost "some skin" after being hauled before the commission.
But they maintain there is no smoking gun.
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