"Most big corporations have their 'Nike moment' at some stage - when they realise the difficulties of maintaining their standards, particularly in an increasingly global environment," FLA president Auret van Heerden said.
"The problem with the supply chain is that it's a moving target."
The move by California-based Apple will intensify scrutiny of its suppliers, including Samsung Electronics, based in Seoul, and Hynix Semiconductor, based in Inchon, South Korea.
The FLA makes unannounced checks on about 5 per cent of its members' supply chains each year, Van Heerden says.
Apple released a list of 156 companies that represent 97 per cent of procurement costs, with its annual report on factories where the iPhone, iPad and other products are made.
In the course of the 229 audits, Apple said it discovered several violations, including instances of underage labour at five facilities. Apple said it required the suppliers to support the young workers to return to school and to improve their management systems to add age-verification procedures. Apple also said it found instances of involuntary labour and stopped working with one of the suppliers involved.
Apple also discovered at least 90 factories with records showing workers were exceeding its maximum of 60 hours a week and at least one day of rest in seven days of work. The company found violations of anti-discrimination rules for workers who were pregnant or had hepatitis B. Apple said it made the suppliers end the discriminatory screenings.
Van Heerden says growing scrutiny of global companies by investors and consumers means they are more likely to insist suppliers introduce best practices in countries where governments are unable or unwilling to do so.
"If you're a 16-year-old girl in a developing country, your best chance of enjoying proper rights is if you get to work at a multinational," he said. "The power of their contract is more powerful than the power of law."
Apple's biggest supplier, Taiwan's Foxconn, has been a subject of scrutiny after at least 12 workers have committed suicide at its plants in China. Three died last year and more than 70 were hurt in blasts at two iPad facilities, one of which was also owned by Foxconn.
In response to pressure from Apple and the media, in 2010 Foxconn more than doubled wages for some workers in China and employed counsellors.
Apple will now subject itself and its suppliers to the FLA's membership criteria, including submitting to audits and enforcing a code of conduct based on standards approved by the United Nations' International Labour Organisation.
Taipei-based Hon Hai Precision Industry, Foxconn's flagship listed unit, gets 22 per cent of its revenue from Apple, data compiled by Bloomberg show. Pegatron earns 16 per cent of sales from the US company.
Efforts to improve conditions have failed to appease some activists and labour groups. Demonstrators at the September opening of Apple's flagship store in Hong Kong called on the company to protect workers' rights.
China Labour Watch last month said the explosion at Foxconn's plant in May and another on December 17, at a factory owned by Taipei-based Pegatron, were caused by ignition of aluminium dust produced by polishing iPad cases.
Independent monitoring isn't the panacea to problems in China's factories, says Geoffrey Crothall, communications director of workers-rights group China Labour Bulletin.
"The problem isn't whether or not they do audits, but whether workers are treated in a reasonable manner," he said. "What the workers need is an effective voice in the workplace."
Apple is more vulnerable than most to damage to its reputation, according to an annual ranking compiled by Interbrand.
The brand was valued at US$33.5 billion last year, the eighth-highest in the world and up from 17th place in 2010, according to the index.
The company's affiliation to the FLA marks a further broadening of oversight for the agency. The association was formed in 1999, primarily by the apparel industry, after Clinton challenged companies and pressure groups to address rising complaints about standards at factories operating overseas, according to its website.
Oregon-based Nike, the world's largest sportswear maker, was a founding member.
Adidas Group, Hennes & Mauritz AB and Juicy Couture owner Liz Claiborne are among 33 participating companies.
Switzerland-based Syngenta, the world's largest maker of agricultural chemicals, sought the FLA's help in 2004 to address concerns over child labour and working conditions on Indian cottonseed farms. Nestle, based in Vevey, Switzerland, in November commissioned the agency to assess the use of child labour and conditions at West African producers of cocoa used in its products such as KitKat and Quality Street candies.
Microsoft said this week that a protest on January 4 by 150 workers at a Foxconn factory in southern China wasn't related to working conditions and the majority of employees who took part had returned to work.
Some had threatened to jump from the roof of a factory building, the Daily Telegraph reported.
- BLOOMBERG