The Fair Work Ombudsman's Harvest Trail Inquiry completed 836 investigations in the past five years, involving 444 growers and 194 labour hire contractors, with the majority picked at random.
More than half of the investigations found breaches of workplace laws including underpayment and failed record keeping.
But the ombudsman believes the full extent of worker underpayments is significantly higher than the $1,022,698 clawed back for workers who follow fresh fruit, vegetables and wine grapes harvests around Australia.
"Our inquiry highlighted unacceptable practices of underpaying workers in one of Australia's largest rural industries," Fair Work Ombudsman Sandra Parker said on Thursday.
Growers rely heavily on overseas workers who commonly do not have a good understanding of Australian work rights and entitlements, the report found.