Hi,
I’m creating a website for a non-profit organisation and they want to have a section for “our partners” with logos of different organisations they sometimes work with or alongside.
Does anyone know if it can legally be an issue to put their logos on without prior consent? they tried emailing these organisations but only very few responded.
I dont see why it should be an issue.
They are not claiming to ‘own’ the logo, they are just using it to refer to that business, which is what a logo is for.
Except if i didnt understand your question 
One organisation who they want to put as part of it had a line on their website saying you may not use our logo without prior permission…
I would think they are best off getting permission so as not to run into issues in the future… Most companies would be happy with the advertisement on another site! 
You should get written consent. Most organizations will be happy to give permission as long as they align with their values, though you need to be sure.