The Conservative government says Bev Oda's apology in the Kairos controversy closes the matter, but the opposition isn't convinced. (Sean Kilpatrick/Canadian Press)

International Co-operation Minister Bev Oda was right to deny a church-backed aid group funding even though she ordered a document altered in the process, Prime Minister Stephen Harper said Tuesday.

"These kinds of decisions are the responsibility of ministers," Harper said during question period in Ottawa. "When we spend money on foreign aid, we expect it to be used effectively for foreign aid, and that's the decision that the minister took."

Asked by Liberal Leader Michael Ignatieff why he hadn't demanded Oda's resignation, Harper said the action was "her decision ... as it was supposed to be.

"Those are decisions that ministers have to make, that they have to be responsible for," he said. "It is not the decision of appointed officials and it is not the entitlement of outside organizations."

Oda was in the House but did not answer questions from the opposition.

She told Parliament on Monday that she was the person who directed that a recommendation from her staff be altered to deny funding to Kairos, an aid agency that counts the Anglican Church of Canada, the Evangelical Lutheran Church in Canada, the Presbyterian Church in Canada, the United Church of Canada, the Quakers, the Mennonite Central Committee Canada and several Roman Catholic bodies among its members.

The minister was backtracking on previous statements in which she said Kairos had lost its funding because the group's work no longer fit with the Canadian International Development Agency's objectives — suggesting she was acting on her department's recommendation.

Oda noted that the opposition has asked Speaker Peter Milliken to investigate whether she deliberately or knowingly misled the House.

"At no time have I stated that the decision for funding was that of the department," Oda said Monday. "I have repeatedly and clearly stated in response to questions in the House and at a committee, that the funding decision was mine.

"If some were led to conclude that my language implied that the department and I were of one mind on this application, then I apologize."

PMO involved: Rae

'Anyone who knows anything about the Harper government will know that none of these ministers are what you would call autonomous actors,' Liberal MP Bob Rae says. (Sean Kilpatrick/Canadian Press)

Earlier Tuesday, Liberal MP Bob Rae alleged that Oda had the document doctored under orders from the Prime Minister's Office.

"Minister Oda could not have done what she did without instructions from the Prime Minister's Office and, for all we know, from the prime minister himself," Rae told reporters at a news conference.

"Anyone who knows anything about the Harper government will know that none of these ministers are what you would call autonomous actors."

The government said Oda apologized, closing the matter. But opposition MPs weren't satisfied and some say she should resign.

"When Maxime Bernier left his documents, he had to resign," NDP MP Paul Dewar told reporters Tuesday.

Bernier resigned as minister of foreign affairs in 2008 after he was revealed to have left classified documents at the home of his former girlfriend, who had previously been linked to the Hells Angels.

But in an interview with CBC News on Tuesday, Dewar said Bernier committed a "clumsy act," whereas Oda's actions warrant more scrutiny.

"She was very clear she directed someone to alter a document," he said. "That's extremely, extremely serious."

Tom Flanagan, Harper's former chief of staff, called on Oda to resign.

"She clearly fibbed to the House when she said that CIDA was in favour of defunding Kairos, when it's a political decision," Flanagan said on CBC's Power & Politics with Evan Solomon. "She should have stood up and said, 'This is our political decision.'"

"By trying to make it appear to be bureaucratic advice now, she’s created this long-running soap opera," he said.

"It’s amateurish from start to finish. Is it very serious? Not really," Flanagan added.

'We stand by these decisions'

In 2009, Immigration Minister Jason Kenney said Kairos lost government funding because it had taken a position against Israel. Kairos has responded that Kenney was wrong about the organization's stance. (Sean Kilpatrick/Canadian Press)

In December 2009, shortly after the decision to axe Kairos's funding was made, Immigration Minister Jason Kenney spoke in Jerusalem to the Global Forum for Combating Anti-Semitism. He said Kairos lost its funding for "taking a leadership role in the boycott … divestment and sanctions campaign" against Israel.

"We're receiving a lot of criticism for these decisions," he said. "I can't recall how many times I've been sued for some of the decisions that we have taken. But we believe we have done these things for the right reasons and we stand by these decisions."

Kairos denied taking a leadership role in the boycott campaign a few days later.

Kairos's board of directors decided in 2007 "against advocating sanctions against Israel or a boycott of products from Israel," the statement said.

Member churches and organizations were free to choose to divest from a Canadian corporation in the region "that is contributing directly or indirectly to the violence, occupation or other human rights abuses" as a "last resort," the statement said.

Kairos also said it has a "fundamental position of support for the right of Israeli people to a safe and secure state, alongside a viable and secure Palestinian state."

In an interview with Radio-Canada Tuesday, Kairos executive director Mary Corkery said Kenney's comments to the anti-Semitism conference were misleading.

"We think he had us confused with Kairos Palestine, and Kairos Palestine actually released a document a week earlier in which they expressed the passion of the Palestinian Christians for an independent state and for peace. And in that, they asked people around the world to consider supporting their call for boycot, divestment and sanctions as economic measures to bring about peace.

"Kairos in Canada has never adopted that action," Corkery said.

Kairos Canada represents 11 churches and church organizations in Canada. There is no organizational link between Kairos Canada and Kairos Palestine, although some of Kairos Canada's partners signed on to the Kairos Palestine statement, according to a Kairos Canada spokesperson.

"Kairos" is a Greek word that means "crisis" or "important time," and is often used by church organizations for urgent campaigns.