The money is on top of annual funding of £2.67 million from the Scottish Government and means they will be able to start to re-open in the autumn, with safeguards in place to protect visitors and staff.
Glasgow Science Centre, Dynamic Earth in Edinburgh, Dundee Science Centre and Aberdeen Science Centre collectively attract around 700,000 visitors and engage with 1.5 million people of all ages annually.
Since closing their doors in March, the centres, which employ 400 members of staff, have continued to engage with school pupils, teachers, families and the wider public.
Science Minister Richard Lochhead said: “Our science centres are a valuable national asset and, even though they are currently closed to visitors, they have continued to deliver STEM learning opportunities through the innovative use of online learning.
“From daily online videos and weekly themed home-learning programmes to stay-at-home science and STEM care packages, they have been providing valuable resources to support parents, teachers and young people.
“Science, technology, engineering and maths impact our everyday lives.
“This has never been more relevant than in the current global pandemic.
“The huge contributions of Scotland’s STEM-related research and industry have being highlighted nationally and internationally throughout the Covid-19 crisis.
“This extra money puts our science centres in a stronger position to continue to showcase Scottish research and industry excellence in STEM, inspiring our young people and supporting their learning, while helping Scotland realise its ambitions as a science and innovation nation.”