A Flagship Scottish ­Government education ­policy aimed at enhancing the country’s international reputation in science and modern languages has been dealt a damaging blow.

New figures show a worryingly low number of schools opting to take new baccalaureate qualifications.

The Scottish Qualifications Authority said only 13 secondary schools out of a total of 376 had registered for the languages qualification by the deadline at the beginning of October – less than 4% of the total. In addition, only 63 secondaries – just 17% – have signed up for the science baccalaureate.

The SQA said most schools were from the local authority sector, with just four private secondaries applying.

The figures will come as a disappointment to Fiona Hyslop, the Education Secretary, who said the new qualifications would encourage more pupils to study science and languages at a higher level, prepare them better for university and would become an international benchmark of quality.

In December last year, a major international study found that Scotland’s school pupils were lagging behind England and other international competitors in maths and science.

Academics found that primary pupils in Scotland were ranked 22nd for maths and 23rd for science in a league table of 60 countries, while secondary pupils were 15th for science and 17th for maths.

There is also concern that industry cannot find enough qualified engineers while globalisation has increased the demand for linguists.

Last night, opposition politicians and teaching unions questioned the merits of the science and language baccalaureates.

Rhona Brankin, education spokeswoman for the Scottish Labour Party, said: “The SNP has mismanaged this entire process and it is no wonder that the take up is so poor.

“So far, Ms Hyslop has come up with a title for this new qualification, but she has failed to put the right system in place to make it attractive to schools.”

Liz Smith, education spokeswoman for the Scottish Conservative Party, said: “Until we know what university recognition there will be for these qualifications there will not be a huge take-up because it doesn’t have any particular worth or value before that happens.”

Ann Ballinger, general secretary of the Scottish Secondary Teachers’ Association, said schools were yet to be convinced the new awards added “value” for pupils.

“We would welcome anything that encourages pupils to take up science and languages in greater numbers, but it is not clear what extra value these new awards give to pupils,” she said.

However, a spokesman for the Scottish Government said officials expected the qualifications to become more widely available for pupils over the next few years.

“We know it takes time for new qualifications to become embedded in the education system and it would therefore be unrealistic to expect a large proportion of schools to be offering the

baccalaureate during its first year,” he said.

“We also encourage local authorities to provide collaborative arrangements, where pupils can study a subject at a different school in the local area when that subject is not on offer at their own school.

“Historically in Scotland science subjects have always been more popular than ­languages, and so it should not be surprising that initially more schools are offering the science baccalaureate.”

A spokesman for the SQA said: “We are staging support events for the new awards and these continue to be attended by schools and colleges which have not yet signed up, but are keen to learn from the experience of those which have.”

The baccalaureates were first highlighted in the SNP’s 2007 election manifesto.

The party said it wanted to examine the potential of the highly-respected International Baccalaureate, but a crucial first step was to introduce an award based on existing Highers and Advanced Highers.

In addition, pupils will also have to undertake a ­specialist project in sixth year, in collaboration with industry or higher education to qualify for the award.

However, because the baccalaureate was essentially based on the recognition of a pupils’ existing Highers and Advanced Highers, many simply saw it as “window-dressing”.