He contested and won the Kudat seat on a BERJAYA ticket in the March 1981 state election and was appointed Assistant Minister to the Chief Minister of Sabah the following year. He held the post until April 1985 when he lost the seat to Wong Phin Chung of United Sabah Party (PBS).
In March 1987, he became a member of the Berjaya Supreme Council but later left the party when it became clear that it was losing ground.
Chong and several Chinese leaders founded the LDP in 1989 and was made its pro-tem secretary general. Then in 1991, he became the party's president. He did not contest the 1994 state election but a year later was appointed Senator in the Dewan Negara, and subsequently included in the Cabinet of Malaysia as a Minister in the Prime Minister's Department. He quit the federal ministerial post in March 1999 to contest the state polls. This time, he won back his traditional stronghold of Kudat, and was appointed state minister of Tourism Development, Environment, Science and Technology.[1]
When Musa Aman took over the helm of the state government in 2003, Chong was appointed Deputy Chief Minister as well as the person in charge of the tourism, culture, and environment portfolio. It was then the rotation system was scrapped and from then onwards, the Chief Minister post was held by the United Malays National Organisation.
In April 2007, Chong resigned from the Deputy Chief Minister post under Musa Aman's cabinet, citing matters of principle.[2][3]