The move comes after an outcry about public funds going to support alternative therapies that have not been proven effective.
Terre Sans Frontières (TSF) had been given C$200,000 ($149,000, £114,000) over five years to provide homeopathy in the Central American country.
Around the world, alternative medicine charities modelled after Doctors Without Borders are still going strong.
The Quebec-based charity had been funded through Global Affairs’ Volunteer Cooperation Program, which helps send skilled volunteers to developing countries.
“We will not be supporting such projects in the future,” said Louis Belanger, spokesperson for the ministry of international development.
TSF’s programme in Honduras sent homeopaths to share information with local primary care providers about how to incorporate homeopathy into their practice.
They also provided homeopathic treatments for Chagas disease, a tropical parasitic disease that can cause flu-like symptoms and lead to life-threatening chronic illness.
Homeopathy is an alternative medicine founded Germany in the late 18th Century that is based on the principal that diluting a substance that causes symptoms can help cure the underlying illness.
So pollen or grass could be used to create a homeopathic hay-fever remedy.
It has been routinely debunked by scientific studies.
“It’s not like there’s an ongoing scientific debate here,” says Tim Caulfield, research director of the Health Law Institute at the University of Alberta.
“It’s like flying carpets. It’s really that level of nonsense.”
Mr Caulfield said he was appalled that the Canadian government would fund homeopathic treatments.
“It’s a waste of money and it’s a waste of money in a context where the money could be spent elsewhere,” he said.
TSF, which could not be reached for comment, is not the only alternative medical charity to operate in developing countries.
Modelled after the popular charity Doctors Without Borders, Naturopaths Without Borders, Homeopaths Without Borders, Herbalists Without Borders, and Aromatherapists Without Borders all send practitioners to developing countries to administer treatments.
The relationship between governments and alternative medicine providers is complex.
In 2018, the NHS stopped funding some homeopathic treatments in the UK.
In 2013, the World Health Organisation recommended incorporating alternative and traditional medicine into mainstream medical policies.
But it specifically advised against promoting homeopathy as a treatment for infections like malaria and HIV.