A total of 1,011 girls studied Higher computing in 2007, compared with 560 last year – a decrease of 45 per cent – the party said.
Comparing the same years, Labour said higher physics saw a 39 per cent drop, chemistry 32 per cent and biology 24 per cent.
Education spokesman Iain Gray said the figures from the Scottish Qualifications Authority (SQA) raised concerns of a skills gap.
Mr Gray said: “The single most important economic investment we can make is in education, and we need to make sure more pupils are studying the key subjects to give them the skills they need for the jobs of the future.
“The SQA’s own information shows huge drops in the number of young women studying key subjects since the SNP came to power in 2007.
“Scotland faces a skills gap of 10,000 digital jobs over the next decade. Filling in that gap will mean a huge windfall for our economy, but missing out will mean Scotland lags behind the rest of the UK.
“The SNP government should be doing more to encourage young women into subjects like computing and sciences, but that will be made all the more difficult by hundreds of millions of pounds of cuts to schools and local services in the SNP budget.”
Labour said the SNP “must use the powers of our Scottish Parliament to stop Tory cuts” to education.
A Scottish Government spokesman said: “We have seen progress in the promotion of Stem [science, technology, engineering and mathematics] careers to girls and women through modern apprenticeships, college and university courses, but these are still areas that see higher than average rates of gender segregation.
“Tackling these stereotypes will help us reduce the gender pay gap and see more women reach the higher levels in these professions.
“Developing Scotland’s Young Workforce will address gender balance in the workforce and we announced an additional £1.5 million for the teaching of these subjects in 2016/17.
“This underlines the Scottish Government’s commitment to improving educational attainment for all young people and we have continued our investment in the CareerWISE programme which gives girls real life work experience in the sector this year.”