Anson Chan Fang On-sang has hinted she might quit if repeatedly asked to enforce decisions that go against her principles and conscience.
In an interview published yesterday, the Chief Secretary also made a veiled attack on local people who invited Beijing's interference in Hong Kong affairs.
Mrs Chan, currently top aide to the Governor and about to hold the same position under Tung Chee-hwa's leadership, said civil servants were not trained just to implement decisions.
'I like to think I'm a loyal civil servant, but loyalty is not everything in my eyes,' she said.
'You're there to give your views without bias. Where a consensus is not possible, then I accept that the Governor, presently, and the chief executive in the future, has the prerogative to make the final decision. When that is made, we have a duty to defend that policy.
'But there might be issues that are points of principle, and, as a matter of conscience, you feel you can't accept those decisions.
'When that happens, you start asking yourself, 'Do I stay or do I go?' And I think most people would know what my answer would be.' Mrs Chan's remarks in Newsweek, come amid speculation that some senior policy secretaries are at odds with their future boss.