Documents from the Canadian Food Inspection Agency obtained through the freedom of information laws indicate tests done in 2009 and 2010 on 178 samples of domestic and imported organic apples showed 23.6 percent had pesticide residue.
Another 112 samples done in 2010 and 2011 were found to have more than one type of pesticide, the CFIA documents said.
Michel Saumur, national manager of the CFIA's organic office, told the broadcaster minute traces of pesticides found suggested growers weren't flaunting guidelines.
"We feel that most of this presence is based on non-intentional contamination," he said.
That was echoed by Matthew Holmes, executive director of the Canada Organic Trade Association. He told the CBC he suspects the pesticide residue is occurring during processing and packing after non-organic apples have been handled.
The most common chemical found in the tests was the fungicide thiabendazole, the report said.