The Bureau of Investigation told AFP that Wu Li-chen, a deputy chief of the bureau, visited Hong Kong last month. It declined to give details.
Wu was thought to be the highest ranking official from the bureau to have visited Hong Kong since 1949, when Taiwan and the Chinese mainland split at the end of a civil war.
Taiwan's state Central News Agency said Wu met law enforcement officials during her three-day visit to the self-governing southern Chinese city beginning April 23.
Wu also visited the Hong Kong Jockey Club, where she was briefed about efforts to battle gambling-related crimes and money-laundering, it said.
The trip would have been unthinkable before 2008 due to high tensions between Taiwan and China.
Ma Ying-jeou of Taiwan's China-friendly Kuomintang party came to power that year on a platform of improving trade and tourism links with the mainland, and was re-elected in January 2012.
Hong Kong opened a liaison office in Taiwan in 2012 and announced that Taiwanese visitors to the city would no longer have to pay a visa fee.