"Lidl Sweden has been informed that cleaning liquids have been poured into the trash to stop trespassers from stealing garbage at one of our stores during a short time period," Mathias Kivikoski, Lidl's chief executive in Sweden, said in a statement.
"We deeply regret what has happened and this is not something the company recommends or permits."
A newspaper in Stockholm suburb of Solna revealed that Lidl employees at a local store had become tired of homeless people searching trash bins had last week begun pouring toxic cleaning products on discarded food.
They put up a sign near the bins warning that the goods had been poisoned, but it remained unclear if anyone had eaten the food, the Mitt i Solna paper reported. Food had disappeared from the bins after the staff began poisoning it.
Rolf Nilsson, who heads a Stockholm homeless organisation, described the employees' actions as "crazy."
"This is just so upsetting and distressing. We're talking about people who have to dig in garbage containers to find food to eat," Nilsson told the Aftonbladet daily.
Lidl in Germany has been plagued by several scandals in recent months including spying on its own employees and cheating its customers out of bottle deposits.