Welsh heads fear their pupils may be marginalised following this week's Tomlinson report, which sets out the biggest reforms of English secondary education for more than half a century.
They are concerned that the proposed reforms could widen the gap between the school-leaving qualifications achieved by Welsh and English pupils and make it difficult for Welsh pupils to study at universities in England.
Brian Lightman, head of St Cyres comprehensive, Vale of Glamorgan, said:
"We have the same university system. My fear is that if England goes in one direction and Wales goes in another, university entrance will be difficult for Welsh pupils."
Anna Brychan, director of the National Association of Headteachers in Wales, agreed.
"Pupils in Wales still want to go to English universities," she said. "If the qualifications develop differently, we need to ensure that they are on a par with each other, and that Welsh qualifications are understood and valued in the same way as those in England."
But Mr Lightman, whose school is piloting the new Welsh Baccalaureate, said he welcomed some similarities between the two systems.
"We're both looking at breadth of curriculum and extended pieces of work," he said. "The pilot has informed the direction Tomlinson has gone in, focusing on communication and basic skills."
The 207-page Tomlinson report, which follows a 20-month Government inquiry, proposes a four-level diploma embracing all secondary qualifications, in which pupils would be assessed mainly by teachers until they reached advanced level.
Vocational qualifications would be improved and absorbed in the new structure and all pupils would have to pass courses in basic literacy, numeracy and computer skills. More "stretching" courses would also be provided for the most able pupils.
Teacher assessment is seen by the inquiry group, led by Mike Tomlinson, the former chief inspector of schools, as crucial to the success of the reforms.
The Welsh Assembly government has welcomed the report and said it reflects many of the developments that have already taken place in Wales. An Assembly spokesman said: "In many respects we are already ahead of the game. There are many parallels to our Welsh Baccalaureate pilot. We are sure there will be a lot we can learn from future development in England, and that England will be able to learn from what we have already done."
He added that the flexibility of the Welsh Bac would allow it to accommodate any revisions stemming from the Tomlinson report.
Gareth Pierce, chief executive of the Welsh Joint Education Committee exam board, said Welsh pupils would not be hindered by developments in England.
"We expect government teams and awarding bodies will look at comparability, so people can still flow between the two systems and into higher education and employment," he said Certain radical aspects of the report could be rejected by Westminster.
Some ministers appear to be unwilling to back proposed changes to GCSEs that would mean most youngsters taking few external tests until they were 18.
Bodies including the General Teaching Council for England, universities, private schools and teachers' leaders have backed the teacher-assessment plan, but Education Secretary Charles Clarke said: "Assessment must and will continue at all levels on the basis of rigorous, trusted and externally marked examinations. A rigorous external assessment regime at 16 is crucial."
Some proposals, such as the replacement of coursework by cross-curricular research that enables pupils to bypass AS courses and vocational-course improvements, will get ministers' backing.