Both nations expressed unhappiness after it emerged that they had been listed in a document that formed part of a training course manual on torture awareness given to Canadian diplomats.
Foreign Minister Maxime Bernier said he regretted the embarrassment caused by the public disclosure of the manual, which also classified some US interrogation techniques as torture.
"It contains a list that wrongly includes some of our closest allies. I have directed that the manual be reviewed and rewritten," Bernier said in a statement.
"The manual is neither a policy document nor a statement of policy. As such, it does not convey the government's views or positions."
Canadian government embarassed
The document - made available to Reuters and other media outlets - embarrassed the minority Conservative government, which is a staunch ally of both the United States and Israel.
US Ambassador David Wilkins said the listing was absurd while the Israeli envoy said he wanted his country removed.
Asked why the two countries had been put on the list, a spokesman for Bernier said: "The training manual purposely raised public issues to stimulate discussion and debate in the classroom."
The government mistakenly gave the document to Amnesty International Canada as part of a court case the rights organization has launched against Ottawa over the treatment of detainees in Afghanistan.
Under "Definition of torture" the document lists US interrogation techniques such as forced nudity, isolation, sleep deprivation and blindfolding prisoners. It also mentions the US detention facility at Guantanamo Bay in Cuba, where a Canadian man is being held.