GP magazine obtained data from two thirds of primary care trusts, showing 31% were paying for patients to use the highly-diluted remedies.
It comes after doctors and the House of Commons' Health Committee called for NHS funding of homeopathy to end.
However, the government has said it is up to local trusts to decide.
The research by the magazine involved sending freedom of information requests to all 151 primary care trusts, which fund local services.
They received 104 responses, with 32 confirming they were funding homeopathy. Of the 72 that did not, 10 had stopped funding it in the last four years.
Previous estimates have put NHS spending on the treatment at £4m a year - this pays for four dedicated homeopathic hospitals and prescriptions.
The findings by GP provoked a mixed response.
Dr Vivienne Nathanson is head of science and ethics at the British Medical Association, which has a policy calling for no NHS funding for homeopathy.
She said: "While the BMA supports the Department of Health view to allow primary care trusts to make their own decisions about how to spend their resources, we are concerned that scarce funding will be spent on treatment that has no evidence base and that may not work."
But Cristal Sumner, chief executive of the British Homeopathic Association, said the spending was justified.
"Many PCTs are still funding it because it is popular with patients and provides a cost-effective alternative when conventional treatments have failed."
Homeopathy is a 200-year-old system of treatment that uses highly-diluted substances, sometimes so none of the original product is left.
It is given orally in the belief that it will stimulate the body's self-healing mechanism.