Rights and Democracy, an agency created by the Conservative government under Brian Mulroney to encourage democracy and monitor human rights around the world, is racked by internal dissent.
A private investigation firm is now installed at the Montreal-based agency, and its three senior managers have been suspended with pay.
Federal opposition politicians and the family of former president Rémy Beauregard, who died in January, are calling for an independent inquiry into the organization.
Rights and Democracy, with an $11 million budget, is supposed to operate at arm's length from government. Problems began last year after the Harper government appointed new board members.
The new members challenged grants being made to three human rights organizations known to be critical of Israel's human rights record, especially in the Israeli offensive in Gaza. The three organizations are Al Haq, based in Ramallah in the West Bank; Al Mezan, based in Gaza, and B'Tselem, based in Israel.
Former Liberal cabinet minister Warren Allmand, a former president of the agency, is critical of the government appointments.
"It's pretty clear to me that the government recently has been packing the board with people who have the biases of the Prime Minister's Office," Allmand told CBC News.
Aurel Braun, a university professor and the new chairman of the Rights and Democracy board, said he wants to bring accountability to the agency.
He also said he thinks two of the organizations that got grants — Al Haq and Al Mezan — have links to terrorism. The third group, B'Tselem, which is Israeli, is biased and undeserving of funding, Braun said.
President dies of heart attack
Beauregard bore the brunt of the new board members' outrage over the grants. He died of a heart attack after a stormy board meeting.
After his death in January, a public letter bearing the names of all of the agency's 47 staff members was sent to Braun and two others saying: "You have lost the confidence of the employees of Rights and Democracy and we unanimously request your immediate resignation."
However, one person's name was put on the list in error, which Braun said means the letter has no credibility.
One international board member — Sima Simar of the Afghan Independent Human Rights Commission — resigned in protest over what she saw as a hostile takeover of the board. Another board member resigned as well.
Asked at a news conference Wednesday about the turmoil at the agency, Foreign Affairs Minister Lawrence Cannon said he plans to look into it, since he is accountable for the money the government transfers to the organization.
"Obviously, there seems to be a governance structure problem here, and so I'll be looking at that," Cannon said.
He said he doesn't intervene in board discussions, however. "Mine is to make sure that this organization is smooth-running and that it functions correctly."