Do I need to ask permission to use image from a publication I am involved in an EU H2020 project in which we are developping some educational and support material for companies to support them in implementing energy effeciency measures. Factsheets will be made available in the form of Powerpoint or Word documents on a platform that companies who have signed up to the platform will have access to. The documents will be made available under a Creative Commons license, so the companies will be able to adapt the documents (Powerpoint, Word) to their specific needs if they need to (e.g. add their logo, simplify or reformulate some parts).

I would like to know how best to proceed to be able to use images (graphs, diagrams or other) from scientific publications in these factsheets. Can we simply use them in our documents by citing the reference, but without asking permission? Or should we ask permission to the author?, university? or publisher (e.g. Elsevier)?
Depends on who's holding the copyright. Whoever has it is the one who gives permission.

Check the first page, in particular the imprint at the top. If it says (c) the authors, then the copyright is held by the authors; if it says (c) the publisher then you have to ask the publisher.