The final report from a three-year study of a batch of KIPP charter schools in the San Francisco Bay Area probes key issues that have sparked debate about the national network of independently run public schools, including student achievement and attrition.

The independent analysis, issued Sept. 16, comes amid wide acclaim for the KIPP network, along with charges that the schools "cream" the strongest students from low-income communities.

The study concludes that the middle schools...