"The Prime Minister reiterated that the appalling treatment of civilians, including Canadian citizens, aboard the Gaza-bound flotilla was unacceptable, and he called for an independent investigation," Carney's office said in a statement on Monday.
Carney, it said, also reaffirmed Canada's opposition to illegal Israeli settlement expansion, settler violence in the West Bank, and violence against Palestinian civilians.
Although Carney last week denounced Israel's handling of the flotilla members, the broad scope of his condemnation on Monday underlines how strained ties have become between Israel and some of its closest allies.
The Israeli embassy in Ottawa was not immediately available for comment.
Activists released after being detained on a flotilla trying to bring aid to Gaza were subjected to abuse, organisers said, with several hospitalised with injuries and at least 15 reporting sexual assaults, including rape. Israel's prison service denied the allegations.
Israel's ambassador to Canada last week told the Globe and Mail newspaper that bilateral government-to-government relations were the worst they had ever been.
Separately, Canadian Foreign Minister Anita Anand said she had spoken to her Israeli counterpart, Gideon Saar, and told him Ottawa would provide Israel evidence of the mistreatment of Canadians on the flotilla.
"I raised that denying Canadian citizens access to consular services while they were detained violates the Vienna Convention and must never happen again," she said in a post on X.
For his part, Saar said he had told Anand the activists had been inspired by Hamas.
"I also highlighted the horrific anti-Semitic wave in Canada - an average of 19 incidents a day.
"The Canadian government must take steps against anti-Semitic incitement and attacks," he said in a post on X.
