Despite the progress made, the FLA said challenges still lie ahead for Foxconn in improving its factories, one of which is reducing employee working hours to 49 a week. Foxconn also still has 165 action items the three factories must address by July 2013. But so far, 89 have already been completed, according to the FLA.

In response to the FLA's report, Foxconn noted in a statement the company was ahead of schedule in meeting the list of changes to improve its factories' working conditions. The company also pointed to how the FLA has cited its role in supporting a new regulation, effective January of next year, to extend unemployment insurance to migrant workers in Shenzhen, China, a major Foxconn manufacturing base.

"Our hope is that our efforts will not only benefit Foxconn, but that they will also serve as a model for other companies and help improve working conditions for the manufacturing industry throughout China," said Louis Woo, special assistant to Foxconn's CEO, in a statement.

The FLA's investigations come as both Foxconn and Apple have received criticism over the years for allegedly allowing poor working conditions at Foxconn factories in China. Earlier this year, The New York Times a story describing those conditions, which brought further criticism and resulted in Apple asking the FLA to audit Foxconn.

While Tuesday's report noted improvements made at Foxconn's factories, New York-based China Labor Watch said the FLA's investigations only looked at selected factories and not Apple's entire supply chain.