The 10-point "guiding principles" for security followed talks with the government after the killing of 17 workers from a French aid organisation in August.
Aid organisations from the US, Japan, Britain and Norway were among 11 countries along with the UN and the European Union which signed the declaration with the government.
"This (agreement) is a promise we are making in difficult times to counter the growing vilification and false accusations against NGOs (non-governmental organisations)," Canadian High Commissioner (ambassador) Angela Bogdan said.
Groups from the countries and organisations work on war-related issues such as refugees and others help with reconstruction from the devastation caused by the December 2004 tsunami which claimed thousands of lives.
Plans to implement the security guarantees were not detailed.
The declaration followed a series of accusations led by state-run media against international and local charities for allegedly supporting the Liberation Tigers of