Headteachers across England, it seems, are furious. And Ron Munson, head of Taverham high school, in Norwich, is among them. "I really do not understand what the government is doing. And why is it doing it retrospectively, without having carried out any consultation, and without having published detailed plans beforehand?" he says.

The object of his ire is the "English baccalaureate" (Ebac), a new GCSE performance measure, being introduced in school league tables to be published tomorrow.

Announced formally only seven weeks ago in the government's schools white paper, this will rank schools on the proportion of their pupils achieving A*-C passes in five subject areas specified by ministers: English; maths; two sciences; ancient or modern history or geography; and a modern or ancient language. In future, pupils will achieve certificates rewarding their performance on this measure, the government says.

This might seem innocuous. But the plans are already provoking serious disquiet in many schools, and not just because tomorrow's rankings will show low proportions of pupils achieving the new benchmark in most institutions.

The national results will show around 15% of pupils hitting the new benchmark, with fewer than 10% in many schools. Many of Labour's academy schools, in disadvantaged areas, are likely to be near the bottom of the rankings.

Hundreds of schools will see drops of at least 40 percentage points in the proportion of their pupils achieving the government benchmark under the new measure, an analysis of last year's results suggests: this lists performance in the individual subjects of languages and science but not on the combined new English bac measure. Last year, more than one in five state secondaries – including 57 of the 123 academies – had fewer than 10% of their pupils passing a modern language at C or better, meaning that achievement on the English bac last year would have been at least as low as this for these schools.

One school spoken to by Education Guardian had more than 70% of its pupils achieving five GCSE A*-Cs, including English and maths, in 2010. This drops to 3% achieving the English bac, caused largely by small numbers of pupils there passing humanities subjects.

Inquiries by Education Guardian have uncovered not only widespread unhappiness among school leaders, but also predictions that the new measure is already leading to radical, and often controversial, changes in the curriculum offered by at least some schools.

The new move seems driven by a concern that pupils have been pushed towards non-traditional academic subjects in recent years because of the way league tables have worked.

With the rankings hitherto centring on the proportions of pupils achieving five A*-C grades, in GCSEs or vocational equivalents, including English and maths, the incentive has been for schools to focus on English and maths and, it is claimed by teachers of these subjects, avoid "harder" GCSEs such as history or languages.

When he first spoke about the English baccalaureate last September, Michael Gove, the education secretary, said it would "dramatically strengthen the position of core academic subjects in our schools, and stop the shift to less challenging courses driven by the current perverse accountability system".

The white paper then set out the government's expectation that "every pupil should have a broad education (the English baccalaureate)".

The coalition government is particularly concerned about the position of languages, the white paper pointing out that the proportion of pupils studying a language dropped from 79% in 2000 to 44% in 2009, Labour having allowed pupils to drop the subject at the age of 14 in 2004.

However, many heads argue that the move conflicts with a drive, promoted by Labour, to offer as broad a range of options to pupils as possible.

In effect, some argue, they are being penalised for following that aspiration under these new league tables, which will show, in many schools, that relatively few pupils now take all English bac subjects. Instead, pupils have opted for subjects such as religious studies, information technology and vocational courses, and even "short-course" language GCSEs, which do not count towards the new measure. Yet the results will suggest that institutions where few pupils achieve the English bac are underperforming.

Heads feel particularly aggrieved that the league tables are being reformed retrospectively, ranking schools on exams taken before the new measure was announced.

Munson says: "The fact that they've done it retrospectively is just crazy. We are talking about a qualification that we knew nothing about, and yet we are being measured against it."

Munson says his current curriculum, praised by Ofsted, offers pupils a "huge amount of choice", with many youngsters opting for vocational qualifications that do not feature in the English bac. Around 99% of pupils are allowed to follow subjects they have chosen, he says.

He says he will resist pressure for this to change now the English bac has been introduced. But many schools would not. He says: "Schools will force pupils to take certain subjects."

There are already signs that this is happening. John Pout, head of Rainhill high school media arts college in Prescot, Merseyside, says that, because of the new measure, as of September, the school plans that the "top half of the year group" starting GCSEs will all take a curriculum designed to give them the English bac.

He predicts that, as a result, a host of subjects, including business studies, ICT, sociology, product design, construction, health and social care and catering, will decline in pupil numbers.

The school currently has some students who have specialised in curriculum areas – by studying more than one language GCSE, or both history and geography. But this will now become very difficult, says Pout, given the time the English bac takes up.

"It will constrain the ability of pupils to specialise in areas of the curriculum they enjoy," he says.

Asked why any school should force pupils to take subjects because of a league table measure, Pout responds: "There is significant pressure on schools to perform through league tables."

The effect on subjects not included in the new measure could be serious.

A senior teacher at a comprehensive in east London, who has extensive contacts with other professionals, says that her school is still undecided over whether to continue to offer citizenship as a subject for 14- to 16-year-olds, given that it will not feature in the new qualification.

The teacher says the school is also unsure about offering the diploma qualification, introduced under Labour, which pupils will find almost impossible to take alongside the English bac. "What do we do? Pull out of all our diploma partnerships even though these have benefited students?" she asks.

More widely, she predicts that many schools will require pupils to take either history or geography. But because most humanities departments are no longer staffed exclusively by teachers trained in these subjects – employing many religious studies and citizenship teachers – many pupils will end up taught by less well-qualified teachers.

Not all schools are unhappy. Carolyn Roberts, head of Durham Johnston comprehensive, in Durham, is quoted on the website of the Association of School and College Leaders saying that, "infuriatingly", she agrees with Gove because league tables have encouraged schools to discourage pupils from taking "harder" GCSEs.

Brian Lightman, general secretary of ASCL, says: "We have had a massive amount of correspondence about this from our members. Some people in quite challenging areas have said that more emphasis on [the English baccalaureate] subjects will be helpful, particularly for pupils who may not have had access to the best universities in the past.

"The rest of the correspondence is very negative about the whole thing.

"The white paper says that tweaking things around the edges is not an option. And yet, here we are, with a curriculum review about to start and with no detailed overarching philosophy having been set out, tweaking things in performance tables. Schools are already changing their curriculums and taking reactive decisions, because of league table pressures rather than through a holistic view of their needs.

"This feels rushed. It's not the way to implement curricular change."

Munson says he is confused as to whether the government wants to force pupils to take certain subjects or not, while he also believes the selection of subjects for the English bac is backward-looking.

He says: "If the government believes modern languages should be compulsory, it should make them compulsory, instead of trying to introduce change by the back door like this.

"And, under the English baccalaureate, someone doing subjects such as Latin and ancient history is going to get recognition for it, while another doing ICT and engineering will not. That's a fine example of a modern, forward-thinking government, isn't it?"

Concerns have also been raised by the Specialist Schools and Academies Trust, which wrote to Gove before Christmas asking him to postpone the new measure's introduction until 2013.

Even some associations representing subjects included within the English bac have voiced reservations. Linda Parker, director of the Association of Language Learning, says there are worries about pupils who did well in many subjects but narrowly missed achieving the benchmark, and also that pupils unlikely to gain a C grade would still miss out on the chance to study languages.

An education department spokeswoman says: "The EBac represents a core that we think all schools should be making available to their pupils. We do, however, recognise that the full range of EBacc will not be suitable for all pupils and that is why we have not made it compulsory. We recognise the wider benefits that studying other subjects and qualifications can bring and we will encourage all pupils to study non-English baccalaureate subjects alongside the core English baccalaureate in order to get a well-rounded education."

League table changes would appear to be easy for ministers to put into effect. But their detailed implications, as Gove is now being reminded, are often complicated and highly contentious.