Nonetheless, as a precautionary measure, it said it was cutting funding to the scheme's "partner schools" throughout Xinjiang province that were the target of the allegations.
"In light of the risks associated with the partner schools, which are widely dispersed and difficult to monitor, the scope and footprint of the project is being reduced," the World Bank said in a statement.
"Specifically, the project component that involves the partner schools in Xinjiang is being closed."
World Bank funding to the five schools directly supported by the project will continue, under "enhanced supervision."
China's treatment of the Uighurs - a mostly Muslim, Turkic-speaking minority concentrated in the tightly-controlled northwestern Xinjiang region - has come under growing scrutiny.
Rights groups and experts say more than one million mostly Muslim ethnic minorities have been interned in re-education camps in Xinjiang, where they are being tortured and forced to renounce their religion.
China initially denied the existence of the camps before admitting to running what it called "vocational education centers," which it presented as necessary to combat religious extremism and boost employment.