Swiss cancer specialist Franco Cavalli did not deny he had treated Harrison at the San Giovanni hospital in Bellinzona, but declined to give details, Sonntagszeitung newspaper said.
The musician was treated for a brain tumour at a hospital in the south of the country, according to Swiss press reports.
Harrison, whose life was threatened when he was stabbed by an intruder in 1999, has had two previous known cancer scares.
Swiss cancer specialist Franco Cavalli did not deny he had treated Harrison at the San Giovanni hospital in Bellinzona, but declined to give details, Sonntagszeitung newspaper said.
Harrison, 58, underwent radiotherapy in May and June, according to the paper.
It was revealed in May that the star had surgery for lung cancer in the United States.
He was said to have made an "excellent recovery" at the time.
The operation in Rochester, Minnesota, had been completely successful, a statement said.
The star was also treated for throat cancer in Britain in 1997 after he found a lump on his neck, which he described at the time as "a warning".
'Smoking'
He had surgery in August that year, followed by two courses of radiation therapy at the Royal Marsden Hospital near London, the UK's leading cancer treatment centre.
He later said: "I got it purely from smoking. I gave up cigarettes many years ago, but had started again for a while and then stopped in 1997.
"Luckily for me they found that this nodule was more of a warning than anything else."
The guitarist and songwriter was almost killed in December 1999 after being stabbed 10 times by an intruder at his home, resulting in treatment for a punctured lung.
The assailant, Michael Abram, was detained indefinitely at a secure hospital after a jury decided he was insane.
The former Beatle made a full recovery from the attack and gave evidence to Oxford Crown Court saying: "I believed I had been fatally stabbed."
Speaking earlier this year, Harrison said: "I had a little throat cancer. I had a piece of my lung removed in 1997. And then I was almost murdered.
"But I seem to feel stronger. I don't smoke any more. I'm a little more short of breath than I used to be, so I don't see myself on stage lasting a full 14 rounds."
In 1998, the News of the World newspaper quoted Harrison as saying his first brush with the disease made him think about how tenuous life could be. He compared it to "a raindrop on a lotus leaf".