Education Secretary Michael Russell has urged chartered teachers who feel undervalued to confront their senior management teams.
But academics warn that those who speak up may get a lukewarm reception; one has recently been disciplined for voicing concerns.
Keith Brown, the Skills Minister, who delivered the Education Secretary's speech to the annual conference of the Association of Chartered Teachers Scotland after Mr Russell fell ill, told delegates they could only make the best contribution if they were valued by colleagues and given the chance to show "leadership in learning".
He added: "I would urge you to challenge your school's senior management team where (these conditions) are not apparent and it is hampering the potential contribution you can make."
But Jenny Reeves, of Stirling Institute of Education, told delegates that chartered teachers often found themselves working in places "where challenging what people say is regarded as rude, disagreeable, not to be done".
The TESS has learned of one chartered teacher who was disciplined this month by a local authority for raising concerns in public about problems with school management.
But Dr Reeves suggested that chartered teachers should have more confidence to challenge the status quo, as they could cite bodies of research and classroom experience. "It might make you more influential - it certainly will make you more difficult to dismiss," she said.
The action research carried out by chartered teachers could be a problem, she said, in part due to pressure from colleagues to ensure it produced favourable answers.
Research by Alison Fox, also of Stirling University, suggests that chartered teachers can shift power relations within a school, but that the ultimate impact on pupils is positive.
Professor Walter Humes of the University of the West of Scotland was encouraged by data from the General Teaching Council for Scotland which showed that many young teachers were signing up for the scheme, while research into chartered teachers revealed "a sense of the growing professional confidence of teachers".
Professor Humes believes chartered teachers "might even become a powerfully subversive force, taking Curriculum for Excellence in directions that its progenitors did not intend".
Mr Brown underlined his support for the chartered teacher scheme, which he set against disappointing results in international comparisons of educational performance.
"What that tells me is that, as a system, we are not getting enough value from your dedication - that we are not setting free your capacity to drive up standards and improve outcomes for children and young people," he said.
Research showed teachers were the most influential factor in pupils' success, he said, and building on the expertise and enthusiasm of chartered teachers was crucial in making Scottish teachers the best they could be. But he did not want to see chartered teachers pulled away from pupils, and backed the Scottish Negotiating Committee for Teachers' code of practice: "The code states very clearly that chartered teachers remain primarily classroom teachers, and at no point should they be regarded as part of a school's management structure."
Mr Brown said the overall picture was improving for chartered teachers, with numbers due to rise above 1,000 next month.
A recent HMIE report made for "much more positive" reading than a 2007 publication by the inspectorate, when a dearth of opportunities to work with colleagues was causing lack of clarity about the role. In one authority, a chartered teachers' network is now promoting their contributions and encouraging schools to share ideas.