His comments come after footage circulated on social media showing what appeared to be long queues at the checkpoint of mostly seven seaters waiting to cross into Shenzhen after midnight.
The tailback stretched all the way to San Tin Highway at one point.
Large numbers of northbound travellers were also stuck in urban areas, with dozens of people lining up for cross-border coach services in Mong Kok.
Many of them had come to Hong Kong for Halloween festivities or a concert in Kai Tak.
Hong Kong Non-Franchised Bus Association chairman Eddie Choi explained that private cars with permits for other checkpoints all diverted to Huanggang after midnight, since it is the only 24-hour crossing to Shenzhen.
Timothy Chui, executive director of the Hong Kong Tourism Association, said there could be even more cross-border revellers next weekend.
He suggested creating dedicated lanes for buses and coaches around the port facility.
Writing on Facebook, Chief Secretary Eric Chan said he paid a visit to the Shenzhen Bay and Huanggang control points following a visit to Dongguan.
Chan said he directed the Security Bureau to continue ensuring that port operations remain safe, efficient, and orderly.
Authorities were told to proactively assess and forecast passenger traffic, and open additional inspection counters and vehicle lanes ahead of peak periods.
Chan also encouraged travellers to consider staying overnight in the SAR for a more comfortable and fulfilling experience.
