Given the global nature of shipping, the IMO is holding talks separate to U.N. climate pact negotiations in which about 190 nations aim to agree by the end of the year a deal to succeed the Kyoto Protocol.
A key committee of IMO is set to meet in July.
Japan's proposal is similar to that of Denmark, but differs from the European Commission's idea to incorporate shipping into a global emissions trading scheme in the medium term beyond the 2008-2012 Kyoto period.
The shipping sector contributes about 3 percent of the world's emissions of carbon dioxide, the main greenhouse gas, and this is expected to keep rising because of growing demand for goods, despite a downturn for now due to global recession.
"It's an alternative proposal to a cap-and-trade scheme," the source told Reuters in a telephone interview.
"We agree with the basic idea to charge bunker fuel and set up a fund to partly return to ships as an incentive to improve energy efficiency," he said, adding the industry was considering how the pooled fund should be used to support developing countries.
An official at the Ministry of Land, Infrastructure, Transport and Tourism, declined to comment.
Japan has said capping emissions in absolute term would be difficult given high volatility in demand for international shipping, in which developing economies play a key role.
Instead, Japan argues the sector should target efficiency improvement of individual ships and support developing countries' efforts to do so.
An IMO meeting in London this week is considering whether countries should be required to report the energy efficiency of new vessels and whether similar requirements are necessary to existing vessels.