BEIJING—Bitcoin exchanges in China are again allowing withdrawals of the virtual currency, having upgraded their systems in response to heightened government scrutiny.

It ends a three-month moratorium that began shortly after regulators launched an investigation into the exchanges and as they threatened to shut down ones that skirt the rules. Authorities were concerned bitcoin could be used to bet on a decline in the Chinese yuan, as well as to move money out of the country, evading controls on capital outflows.

China’s...