Reporters who took jobs undercover at the Pegatron factories found workers regularly exceeded 60 hours a week more than the company's guidance and that standards on ID cards, dormitories, work meetings and juvenile workers were also breached.
(Also see: Apple supplier Pegatron probing alleged labour abuses)
The broadcaster said promises made by Apple to protect workers in the wake of a spate of suicides at supplier Foxconn in 2010 were "routinely broken".
Apple said that it disagreed with the BBC's conclusions.
"We are aware of no other company doing as much as Apple to ensure fair and safe working conditions," the US consumer electronics giant told the BBC.
"We work with suppliers to address shortfalls, and we see continuous and significant improvement, but we know our work is never done."
The company said that it was common for workers to sleep during breaks, but that it would investigate whether they were falling asleep while working.
It also said it monitored the hours worked by over one million workers, and that staff at Taiwanese-owned Pegatron averaged 55 hours a week.
The BBC filmed a health and safety exam at a Pegatron factory in which workers chanted out answers in unison, meaning there was little chance of failing.
The footage also appeared to show workers had no choice to opt out of working nights or while standing.
One reporter had to work 18 days in a row despite repeated requests for a day off, the BBC reported.
The investigation by BBC flagship programme Panorama also found that tin from illegal mines in Indonesia where children work in dangerous conditions could be entering Apple's supple chain.
Apple, which promotes ethically sourced minerals, told the BBC it was attempting to drive changes, and that withdrawing from Indonesian mines altogether would be "the lazy and cowardly path, since it would do nothing to improve the situation".
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