The Fair Labour Association (FLA) will audit several suppliers at the request of the iPhone firm, according to The New York Times.
China's Foxconn, the world's largest maker of electronic components, is among the list of companies facing investigation following a series of accidents at its plants in recent years.
"Workers everywhere have the right to a safe and fair work environment." said Apple CEO Tim Cook. "Which is why we've asked the FLA to independently assess the performance of our largest suppliers.
"The inspections now under way are unprecedented in the electronics industry, both in scale and scope, and we appreciate the FLA agreeing to take the unusual step of identifying the factories in their reports."
The FLA's audit, led by president Auret van Heerden, will cover the suppliers responsible for making 90% of Apple products. Employees at Foxconn's sites in Shenzhen and Chengdu will be interviewed, as will staff at Quanta and Pegatron plants.
Foxconn's Chengdu factory came under scrutiny in May 2011, when an explosion at the site left two workers dead. The company also faced a probe led by another of its clients, Microsoft, following an alleged mass suicide attempt at another of its bases.
Apple says that the results of the first inspections will be published in March.