A team of labour rights experts led by FLA president Auret van Heerden began the first inspections this morning at the facility in Shenzhen known as 'Foxconn City'.
The FLA's inspections will also include Foxconn's factories in Chengdu. Similar inspections will be conducted at Quanta and Pegatron facilities later this spring, and when completed, the FLA's assessment will cover facilities where more than 90 percent of Apple products are assembled.
Foxconn produces electronic components Apple's iPhone and iPad products, alongside products for rivals Microsoft, Sony and Amazon. Foxconn is China's largest private employer.
Apple drew sharp criticism after it posted record quarterly revenues of £46.3bn (£29.3bn) for its first financial quarter 2012, with cash reserves of £100bn on the back of the sale of 37 million iPhones - allegedly made in sub-human working conditions.
Apple has historically been accused of using suppliers with questionable worker welfare and safety records, the latest of which was exposed by a New York Times story following an explosion at an iPad polishing plant.
Foxconn's record is not great, with reports of worker suicides, and a further mass suicide protest last month drawing attention to the unsavoury parts of Apple's business model. Apple's CEO Tim Cook says that FLA will have unfettered access to Apple's businesses, and those of its manufacturing partners.
"We believe that workers everywhere have the right to a safe and fair work environment, which is why we've asked the FLA to independently assess the performance of our largest suppliers," he said.
"The inspections now underway 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 says it will interview thousands of employees about working and living conditions including health and safety, compensation, working hours and communication with management. This will allegedly include the inspection of manufacturing areas, dormitories and other facilities, alongside relevant documentation relating to employment conditions.
Apple first ran into bad publicity relating to workers' rights in 2006 when an investigation revealed widespread abuse of China's labour laws. Apple now performs its own yearly audits and publishes the results in a public report.
The FLA says its findings will be posted in early March on its website, www.fairlabor.org.