The European Commission funds of 985 million euro (£775 million) will come from the European Regional Development Fund (ERDF) and the European Social Fund (ESF).
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The Scottish Government and public sector organisations will contribute additional money to take the total to more than 1.9 billion euro (£1.5 billion).
The funds will be invested into developing a low-carbon economy, promoting international business and tackling poverty.
Infrastructure, Investment and Cities Secretary Keith Brown said: “These programmes will enable us to strengthen our research, development and innovation capabilities and help turn innovation into long-term and sustainable jobs and growth.”
He said that now the funds had been approved they would begin to be committed early next year.
Mr Brown added: “Scottish SMEs will benefit through ERDF-funded initiatives by Highlands and Islands Enterprise, Scottish Enterprise and the local authorities aimed at joining up their support for business and bolstering competitiveness in Scotland, the UK and internationally.
“We need to continue progress on reducing Scotland’s carbon footprint and significant funding has been allocated for the transition to a low-carbon and resource-efficient economy.
“We also share the Commission’s ambitions to alleviate poverty in Scotland, to help those who have employment difficulties find work and to increase the skills of our workforce.
“Through ESF we will invest in education, skills and lifelong learning to ensure our workforce are better equipped to meet the needs of the labour market.
“The funds will also target deprived communities and those who are unemployed or on low incomes, focusing on innovative, adaptive and sustainable solutions to reduce poverty.”
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