The Financial Review has reported a speech to a Westpac forum earlier this month in which Mr Howard called for changes to unfair dismissal laws and a return to individual contracts.
He advocated a return to the laws before WorkChoices removed the "no disadvantage test".
"I think we have to address this issue again," Mr Howard is quoted as saying.
"There is no reason why this country should not go back to the workplace system we had between 1996 and 2005, where you had individual contracts.
"I think it's a great pity that in the last 25 years we have had tax reform, IR reform, we privatised government industries, we've got rid of tariffs and we've freed the financial system... but the one area (where) we have gone backwards is IR and I think that's a great shame."
The report came as Federal Labor's primary vote climbed to a six-month high and Julia Gillard was now ahead of Tony Abbott as preferred prime minister.
Mr Shorten says Mr Howard's comments prove the Coalition remains aligned with Mr Howard's policies.
"Mr Howard has, I think, revealed the intention of the Coalition government to sneak into power and then introduce big parts of WorkChoices," he said.
"Mr Howard is the thought leader of the Coalition. The Coalition think that the Howard years were the glory years of conservative politics, and there's no doubt in my mind that the Coalition will be seeking to introduce parts of WorkChoices.
"At least the strategists in the Opposition Leader's office think that a workplace relations debate is the equivalent to them of eating a bowl of rat poison, even though we know that many in the Opposition, the conservative right-wingers, the hardliners, are itching for that debate.
"We would say to Mr Abbott, let the Coalition run free."
No going back
But Mr Abbott says the Coalition will not go back to the past on industrial relations policy.
He insists the Opposition does not want to revisit the laws which have been blamed in large part for Mr Howard's defeat in the 2007 federal election.
"John Howard is two prime ministers ago ... that was then, this is now," he told reporters in Mackay.
"The Labor Government under the Fair Work Act has put in place individual flexibility agreements.
"I think these agreements need to be made more workable, but there's no going back to the past. We want the Fair Work Act to work better."
But some Liberals, including backbencher Steve Ciobo, are pushing for bigger changes to the Coalition's industrial relations policy.
Mr Ciobo has told Sky News it was ridiculous that individual contracts between employers and employees were illegal.
Mr Shorten said Mr Abbott should spell out what the Coalition's policies will be, including whether it would cut penalty rates.
"There is a myth peddled by the conservatives which says that somehow penalty rates are some sort of after-dinner treat for highly paid blue collar workers, they are not," he said.
"If you look at the retail industry, the hospitality industry, average wages there are barely $50,000 a year.
"Penalty rates are the difference between people making ends meet and not making ends meet."