The Canadian International Development Agency provides money for aid projects abroad on the basis of results, not religion, Fantino said Monday as he came under opposition fire in the House of Commons.
The Canadian Press reported Sunday that Crossroads Christian Communications, a group that produces television programs, received $544,813 in federal money to help dig wells, build latrines and promote hygiene awareness in Uganda through 2014.
"We fund results-based projects, not organizations," Fantino said. "Projects are delivered without religious content, including this particular project."
A spokeswoman for Fantino added: "The government of Canada has funded projects by this organization since 1999."
CIDA said in an email that nearly $389,000 of the money has been disbursed so far, and the agency is monitoring the project to ensure the funds are being spent properly.
It says the money is being used to improve access to clean water and basic sanitation to people who have returned to 10 communities in northern Uganda after years of armed conflict.
New Democrat MP Helene Laverdiere said Fantino's office has become a "black hole" for aid proposals, with many simply disappearing, while those that do get funding don't align with Canadian values.
"Those that are funded are increasingly out of step with Canadians," she said.
"How did Christian Crossroads, an anti-gay organization, get sign-off from the minister to operate in a country which Canada has strongly criticized for persecution of its gay citizens?"
Uganda has been shaken by virulent homophobia in the past; Foreign Affairs Minister John Baird has condemned plans for an anti-gay bill there that could potentially include the death penalty for homosexuals..
Crossroads recently listed homosexuality as a perversion and a sin on its website, although the post disappeared after questions were asked about it.
The organization said in a statement late Monday that it is "not anti-gay" and provides aid "based solely on human need and does not discriminate, nor does Crossroads attempt to influence or lobby foreign governments or policies."
Crossroads also said it "supports the Canadian government's position that strongly opposes the criminalization of homosexuality and violence on the basis of sexual orientation" and welcomes the CIDA review.
Laverdiere said a number of groups which the government dislikes have been cut off, but "religious groups that promote their ideology have Conservative connections."
"This is absolutely bogus," Fantino retorted. "Religion has nothing to do with any of that."
Fantino's response left New Democrat Leader Tom Mulcair incredulous.
"It’s shocking to hear Minister Fantino defending the indefensible, standing up today and defending a group that on its website is attacking something that’s recognized and protected by Canadian law," Mulcair said after question period.
"It goes against Canadian values. It goes against Canadian law. And he can’t defend that."
François Audet, director of the Montreal-based Canadian Research Institute on Humanitarian Crisis and Aid, said he believes Crossroads is far from the only group with controversial opinions that receives CIDA money.
"There is, for sure, other hidden treasures, other organizations who do ideological propaganda with public funding from Canadian aid — and what is worrying is that CIDA does not check this," Audet said in an interview.
Audet said that his own research on how CIDA allocates its funds shows that between 2005 and 2010, funding for religious non-government organizations increased 42 per cent, while secular groups saw an increase of just five per cent.
"I have the clear impression — and I am not the only one in the scientific community — that behind this, there is a deliberate strategy to finance the groups ideologically close to the actual Conservative government," he said.
Also on HuffPost