The man yelled "Listen to me for a change" as he accused Mr Morrison late on Wednesday night of failing to deliver on his election promises.
"This is what you said when you got elected last time: 'We're going help all those people that worked all their lives, paid their taxes'," he said.
"I've had a go, mate, I've worked all my life and paid my taxes.
"You can have a million-dollar house, you can have $250,000 in the bank, you can have negative gearing and franking credits, but a disability pensioner can't have any income."
Independent senator Jacqui Lambie accused the prime minister of being out of touch with Australians, expressing some sympathy for the pensioner.
"People have been doing it really, really tough over the last couple of years. I can tell you, they're on edge. They're angry," the Tasmanian told the Nine Network on Thursday.
"Maybe the prime minister should get out of his office more often and not just election time. Maybe (he) won't be heckled as much."
Mr Morrison has been in a political fight with the Queensland government over a flood recovery package, after Acting Premier Cameron Dick said the Commonwealth's refusal to jointly fund a new homes package was "the highest level of disrespect".
"He has made the political calculation he does not need to votes of flood impacted families in this state," Mr Dick said.
But now Mr Morrison has agreed to a 50-50 funding arrangement, despite maintaining it was something the Queensland government should be doing.
He also accused the government of not spending the money already given to it by the Commonwealth.
"We need transparency, these big announcements and commitments are made by the Queensland government, but how much have they actually paid to people?" he told Brisbane radio 4BC.
"They want to play politics with this. I don't want to play politics with this. I just want to make sure people are getting the support that they need."
Mr Morrison said he agreed to the funding arrangement with a degree of caution given the political attacks that arise on the eve of an election.
"Normally, we've worked very closely with the Queensland government and have worked throughout the course of the floods," he said.
"But as we're coming into this election, I think people can see what's going on here."
Assistant Attorney-General Amanda Stoker said she was concerned there was a "very dirty attempt to character assassinate a very good man".
"Ever the optimist, I hope that both colleagues and competitors will behave consistently with their better values," the Queensland senator told AAP.
"But I also really believe that Australians have a good radar for bull and a good radar for games and that they'll see straight through it."
Mr Morrison has had a tough couple of weeks, after a revelations a range of Liberal party members - including NSW Senator Concetta Fierravanti-Wells - had attacked his character and trustworthiness.
The senator accused Mr Morrison of using a rival candidate's Lebanese background against him during a 2007 push to win pre-selection for his Sydney seat of Cook.
Mr Morrison strongly denies this but the man he ousted, Michael Towke, blames him for losing his pre-selction.
"At the time (Mr Morrison) was desperate and it suited him to play the race card," he told Network Ten's The Project on Wednesday.
Senator Fierravanti-Wells also used parliamentary privilege to brand Mr Morrison an "autocrat" with "no moral compass" and "unfit for office".
The May federal election is due to be called within days.
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