The Council of Europe said that users must be informed when filtering is taking place and must be able to control the filtering, switching it off or correcting inaccuracies when they want to.
Filtering content without such safeguards runs the risk of undermining people's human rights, particularly their rights to free expression and information and the right to participate in democratic processes, it said.
The Council of Europe is distinct from the European Union and has 47 members to the EU's 27, and is the body behind the European Convention on Human Rights and the European Court of Human Rights.
The Council's Committee of Ministers has published a recommendation on internet filtering, an increasingly common practice amongst organisations worried about unsuitable content published online.
"When confronted with filters, users must be informed that a filter is active and, where appropriate, be able to identify and to control the level of filtering the content they access is subject to," said the recommendation. "Moreover, they should have the possibility to challenge the blocking or filtering of content and to seek clarifications and remedies."
The Council recognised the need for filters in relation to children's use of the internet, and said that institutions such as libraries and schools should be able to filter content to protect children from potentially harmful content.
It said that there were legitimate concerns about children's exposure to content (for example violence and self-harm, pornography, discrimination and racism) and behaviours (such as grooming, bullying, harassment or stalking) carrying a risk of harm".
It said, though, that countries must ensure that filtering is not used to suppress information or prevent communication. The Council recommends that countries legislate to protect users' rights of access to information.
"Member states should introduce, where appropriate and necessary, provisions under national law for the prevention of intentional abuse of filters to restrict citizens’ access to lawful content," said the recommendation.
The recommendation does not deal directly with the issue of the filtering of illegally copied material from traffic by internet service providers.
Such filtering has been promoted by music industry bodies as a way of stamping out illegal music downloading.