Mr Shorten said one in 10 of Australia's 2.5 million pensioners would be affected by the change.
"They are going to have a marginal change and their part pension goes up as a result," he told Channel Nine.
On Tuesday, Labor announced a plan to abolish cash-back dividend imputation that stops tax refunds being paid to more than 1 million Australian retirees and shareholders who don't pay tax on their income, plugging a $5 billion annual hole in the budget.
But concerns about dividend imputation have been held at the highest levels of the Coalition - not just the Treasury department - for up to a decade, Fairfax Media can reveal.
Prime Minister Malcolm Turnbull commissioned a review of dividend imputation when he was shadow treasurer in 2009.
Mr Turnbull has never released the secret review of Commonwealth, state and local taxes, but it proposed raising the funds to pay for a flatter tax system through abolishing several existing tax breaks and deductions.
He ordered economist Henry Ergas undertake the review in the hope that it would "enable a fairer and more efficient tax system" under a future Coalition government.
Dividend imputation was third on the list of Mr Turnbull's targets for investigation after income and company taxes, but none of the reforms suggested by the Ergas review were acted upon and were pushed to the side after Labor's Henry tax review in 2010.
On Wednesday, Fairfax Media revealed Treasury had been working on changes to dividend imputation ahead of the next May budget, including withholding dividend cheques from non-taxpaying shareholders, before Labor announced the surprise measure this week.
The Prime Minister's office declined to release further details of the Ergas review on Wednesday, while Mr Turnbull accused Labor of "robbing pensioners and self-funded retirees".
"This is an attack targeted at middle-income Australia and people on low incomes," he said.
Treasury analysis of Tax Office figures leaked to News Corp suggest that up to 5000 Australians collecting more than $180,000 a year in taxable income would lose $20,000 in refunds, while 610,000 people on less than $18,2000 a year would lose $800 a year in cash returns.
Former prime minister Tony Abbott said on Wednesday that Mr Turnbull had a "credibility gap" when it came to defending superannuation, because of now-dumped retrospective changes it proposed in 2016.
"The last change to super was an adverse one and it was by the Turnbull government just before the 2016 election," he told 2GB radio.
"To stop a Shorten government there's got to be a more effective attack and the difficulty is ... there is a bit of a credibility gap here, and this is what needs to be addressed."