Riverside Cafe owner Bryan Molnar said last week he had hired extra staff to clean up after the dirt and mess from the construction.
"We've had to employ more staff doing less turnover just to keep the place clean," Mr Molnar said.
Opposition Tourism spokes- man Paul Papalia said it was not fair for traders. "The (State) Government is offering two years rent-free for new businesses at Elizabeth Quay," Mr Papalia said.
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READ NOW"The people at Barrack Street Jetty deserve compensation or rent relief at least equal to what is being offered to new competitors," Mr Papalia said.
A spokesman for Transport Minister Dean Nalder said the Government had provided three months rent relief to affected Barrack Street traders from July 1.
"We have empathy for the conditions they are trading under," the spokesman said.
"The Minister for Transport has already approved ongoing financial assistance for seven traders who have provided proof of financial affect."
The spokesperson said businesses were asked to submit profit and loss statements for independent assessment to have the relief backdated to July last year.
Golden Sun Cruises owner Bill Edgars said he had worked at Barrack Square for 33 years. "My tax turnover was $840 000 in the year ending 2012 and I've just put in |$178,000. Thanks Barnett," Mr Edgars said.
The spokesman said the Transport Minister had arranged to meet with traders next month.
Perth MHR Alannah MacTiernan said the works had fundamentally changed the nature of the business and the government had an obligation to compensate.
"Elizabeth Quay is a good project . . . but we are saying you cannot expect people to be paying the rent they were beforehand," Ms MacTiernan said.