The paper suggests trustees should consider whether the outcome of the referendum will have a direct impact on the work of the charity and its beneficiaries, whether engaging in the debate would further the charity’s purpose and whether it would be a reasonable and effective use of charitable resources.
It also suggests considering the reputational risks of engaging publicly in the debate and how charities would manage those.
The paper, which was written by the charity consultant Belinda Pratten, discusses the major issues of the EU debate and concludes there is very little evidence to judge whether EU policies and directives have had any impact, positive or negative, on voluntary organisations.
"Therefore for the sector as a whole it is hard to say how life would change if we were to leave the EU," it says.
"However, this might be a more pertinent question for particular sub-sectors: how would life change for children’s charities, for example? This is an aspect of the debate that has yet to be aired and it is perhaps one where voluntary organisations can make the most useful contribution.
"Not by taking a stand for or against remaining in the EU, but by thinking through the potential benefits and risks of either option for their charity and its beneficiaries, and then communicating these, where appropriate, in line with guidance from the Charity Commission."
Sir Stuart Etherington, chief executive of the NCVO, said that some charities would believe the outcome of the referendum would have little or no bearing on their activities, but others would foresee important consequences for their activities and would therefore be failing their beneficiaries if they did not speak out.
He said: "While the outcome of the referendum will be directly relevant to a number of charities and some will be considerably affected, all charities will want to consider the implications for the people and causes they support.
"This paper seeks to frame that discussion and assist organisations to think this through – weighing up the potential benefits and risks of either option."
The Charity Commission last month revised its guidance charity campaigning in the run-up to the referendum after it was criticised by charity bodies for using the wrong tone and by the charity law firm Bates Wells Braithwaite as "misrepresenting the law".