The death toll from the accident, which occurred at around 8:30 pm local time on Monday, has risen to 37, with over 100 people injured, the BBC reported.
As many as 28 people were declared dead at the site of the crash off Lamma Island, while others were later pronounced dead at the hospital to which they were taken.
Rescuers are still searching for survivors.
Three of the arrested crewmen worked on a vessel owned by a power company, Hong Kong Electric, and the other three crewmen were from the other vessel involved in the collision. Police have not ruled out more arrests.
"Police arrested six individuals. They are being investigated for endangering people's lives at sea," said Hong Kong's Security Minister Lai Tung-kwok.
The works vessel was carrying up to 120 passengers -- staff and family members of the power company -- who were on a pleasure trip to watch a fireworks display over Hong Kong's Victoria Harbour to mark China's National Day.
After the collision with the passenger ferry, the works vessel capsized quickly. Only its bow showed above the waterline.
Although Hong Kong is one of the busiest shipping hubs in the world, major accidents are rare. Investigations are under way.