AN ALTERNATIVE sewage disposal system for Hong Kong proposed by the private sector is facing stiff opposition from government departments which say existing plans would be more cost efficient. The alternative plan proposes full treatment of all waste being pumped into the harbour by 1997. But the Government's blueprint would result in semi-treated sewage being pumped into the harbour until 2003. The new plan, proposed by Trafalgar House, is facing resistance because, although it would cost the same to build, it would be more expensive to operate. The project is part of the Government's $20 billion master plan to give Hong Kong a modern waste disposal system. Consultants appointed by the Environmental Protection Department are conducting a technical review of the alternative schemes, but government sources say the Trafalgar House proposal is unlikely to be approved. The Hong Kong Land subsidiary proposed as far back as October that pumping semi-treated sewage through an ''outfall'' pipe off the coast of Zhuhai could be avoided by upgrading proposed treatment facilities on Stonecutters Island. The Trafalgar House scheme would cost $11.6 billion to build compared to $12.1 billion for the Government's proposal. The estimated annual operating costs of the two projects are $260 million and $150 million respectively. A source close to Trafalgar House said: ''We are talking about an extra $100 a year for every Hong Kong resident. Is that too much to pay for a system that stops semi-treated sewage being pumped into the harbour until at least 2003?'' But Sui Chin, the recently-retired director of the Drainage Services Department, said cost was the Government's principal concern. ''I appreciate their [Trafalgar House's] enthusiasm for the project, but our main responsibility is to ensure the Hong Kong taxpayer doesn't end up saddling an even larger bill,'' he said. Fiscal limits and a commitment not to fund the project through borrowing made it difficult for the Government to accept the revised proposal from Trafalgar House, he said. Under the Government's scheme, which has already been presented to the Legislative Council, a preliminary sewage treatment works costing $5.3 billion would be built on Stonecutters Island. Removing approximately 60 per cent of the solid waste, the semi-treated sewage would be discharged into the harbour. Stage Two of the Government's Strategic Sewage Disposal Scheme would involve the construction of a pipeline to dump the sewage off the coast of Zhuhai. The Zhuhai authorities have already protested and recently established a marine environmental zone off the coast. The Trafalgar House project eliminates the need to build an outfall pipeline.