"I have directed officials to change course and to review alternatives to deliver medical supplies to the victims of the Assad regime in Syria," Baird told reporters at Ottawa's airport just minutes after greeting German Chancellor Angela Merkel. "The current arrangement will no longer be pursued."
"The purpose of this funding was to help the people of Syria who've been targeted by the Assad regime and not to support such things as warehouses and infrastructure and we'll be working to ensure that aid gets to those people who need it as quickly as possible," Baird said.
Baird announced over the weekend that a group called Canadian Relief for Syria would be given the money to provide medical care to people caught up in the ongoing conflict in the Middle Eastern country.
The newly-formed group said the money would be used to purchase supplies for their network of doctors and nurses on the ground.
Baird said after the announcement was made his department sat down to hammer out the details of the contribution agreement and "that's where we saw some of the issues which caused us some concern."
He said his department has already been in touch with allies, including Turkey, the United Kingdom and the United States, to find ways of delivering medical supplies and care in Syria.
Earlier today, Baird had defended the decision to give money to the group, which was only established earlier this year and does not have charitable status in Canada, saying the money was intended to provide badly needed urgent and primary health care for victims of the violence.
Syria a 'top priority' for Baird
Following the weekend announcement, questions were raised about how a new group with relatively little experience got such a big pledge of money rather than more established charities such as the Red Cross.
Prime Minister Stephen Harper was asked about the decision on Monday and said he had been told by officials that "due diligence" is done on all organizations that are selected for funding.
Questions were also raised about Canadian Relief for Syria because of its connection to another charity called Human Concern International. HCI has faced controversy in the past over its links to the father of Guantanamo detainee Omar Khadr, Ahmed Said Khadr, who helped finance al-Qaeda when he was HCI's representative in Pakistan and was later killed in a gun battle. HCI has never been charged with any terrorist activities, and the organization says it now has better checks on its operations.
Representatives of Canadian Relief for Syria say it is working co-operatively with HCI and it is helping it collect donations for relief efforts. Canadian Relief for Syria is in the process of applying for charitable status, which would allow it to issue tax receipts to donors.
Opposition critics reacted to the funding reversal by saying the government didn't do its research and was making policy decisions "on the fly."
"I'm quite shocked frankly that this government didn't do its homework," the NDP's foreign affairs critic Paul Dewar said on CBC News Network's Power & Politics.
Momtaz Almoussly, a board member of Canadian Relief for Syria, was reached by CBC News and said he wasn't aware of Baird's decision to pull the funding. He said his group has a network of medical practitioners on the ground in Syria.
Baird said the situation in Syria is a "top priority" for him, his department and for Canada's allies. "That's why we'll be moving as expeditiously as we possibly can."
No money had yet been transferred to Canadian Relief for Syria.