Emissions from ships have overtaken power plants as the biggest source of sulphur pollution.
Ships are already the main emitter of nitrogen oxides and suspended particles.
Secretary for the Environment Wong Kam-sing said new emission data, to be released shortly, showed vessels added sulphur dioxide to this list in 2011.
Chief Executive Leung Chun-ying is widely expected to announce measures in his policy address next week to deal with emissions from ocean-going vessels, local ferries and ships.
Power plants used to be the largest emitter of sulphur dioxide, because of the fossil fuel they burn to generate electricity. However, the situation has changed in recent years.
Marine pollution has been steadily increasing, while power plants have cut emissions since 2010 by using scrubbers that remove pollutants before they are released into the atmosphere.
In 2010, power plants accounted for 50 per cent of the city's sulphur emissions, while marine sources constituted 48 per cent, or 16,900 tonnes.
Vessels became the largest emitter of nitrogen oxides in 2010 and for respirable suspended particles in about 2005, sharing 32 and 36 per cent of the pollutants' emissions in 2010, respectively.
Speaking at a meeting organised by think tank Community Development Initiatives on Thursday night, Wong said the new figures would show marine pollution needed to be addressed, along with roadside pollution.
"Both roadside and marine pollution should be dealt with at the same time," he said.
Wong would not be drawn on whether Leung would introduce mandatory measures to clean up marine pollution, which scientists say is harming people living close to the city's busy container ports and piers.
But he said the problem would not be adequately addressed by the voluntary Fair Wind Charter, joined by major shipping lines which pledged to use low-sulphur fuel as they approach and berth in the city.
He said it was not a "level playing field", as not all shipping lines had signed up to the charter. Wong also said "stronger" measures were needed to tackle emissions from both buses and diesel commercial vehicles.
"Voluntary schemes might not be the best - we might need something stronger," he said, referring to the disappointing scheme to encourage the earlier replacement of polluting diesel vehicles with greener models, introduced in the past year.
Wong said he was also in talks with the Transport and Housing Bureau on addressing pollution from franchised buses.
In 2015, only low-emission buses will be allowed to operate on busy corridors in Causeway Bay, Central and Mong Kok.
The buses will also be retro- fitted with devices to reduce the emission of nitrogen oxides.