Air pollution reached its highest level in two years in August.
Hong Kong says it is introducing an incentive program for vessels using cleaner fuel when berthing in its waters.
The three-year program, which starts September 26, 2012 offers a 50 percent reduction in port facility and light dues for ocean-going vessels that make the switch from high sulfur bunkers to fuel with a sulfur content of less than 0.5 percent.
All calls to Hong Kong - about 32,500 in 2011 - are subject to dues based on tonnage of $5.50 per 100 tons.
The new policy is part of a wide-ranging effort to improve the air quality in Hong Kong, which monitors air pollution closely.
Wong Kam-sing, secretary for the environment, Hong Kong
Reducing marine emissions is one of our priorities
"The government has been implementing a package of 22 measures, targeting various major polluting sources, with a view to improving the air quality in Hong Kong," said Wong Kam-sing, Hong Kong's secretary for the environment.
"Reducing marine emissions is one of our priorities and the launch of the incentive scheme is a step forward to achieving this goal."
The former British colony experienced its worst day of pollution in two years last month, driven by emissions from coal-fired power stations, traffic, and factories in China's neighbouring Pearl River Delta, according to Reuters.
Air pollution is a major source of worry for citizens and foreign businesses, with the area identified as one of the worst in the world for air quality.
The International Maritime Organisation has called on all vessels to adopt the 0.5 percent sulfur standards starting in 2020.