The body currently spends £10m with RR Donnelley under the Design, Print, Publishing and Associated Services contract (DPPAS), producing around 1300 publications.
The government said it hoped that by publishing material online and offering printed products on-demand, it would reduce costs and benefit the environment. It will also seek to encourage the use of online versions over print by introducing a nominal cover price for reprints of some publications.
It has insisted that it will maintain the same level of accessibility of its publications, and said key publications would still be printed and distributed to the general public.
Cabinet secretary for finance and sustainable growth John Swinney said: "We must make every effort to ensure that business practices achieve the best investment for Scottish taxpayers. This requires tough, responsible decisions in terms of how we run our public services.
"All Scottish government publications aimed at the general public will still be distributed by hard copy and in the usual way with copies available to download free of charge from our website. We will review these changes to assess their impact over the next two years."
The new regime will come into effect from April.
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