Some are taking a "zero tolerance" approach to alleged abuse by removing whole families without warning, after a dispute with just one individual, according to the worrying report.
The Ombudsman found such action was often "unfair and disproportionate."
'De-registration' complaints accounted for more than a fifth (21 per cent) of all complaints investigated about GP surgeries - up from 15 per cent in 2009-10.
In one case, a practice removed two sisters and their terminally ill mother after one of the daughters, a registered nurse, decided to change the battery in her mother's anti-sickness medication device. Strictly speaking, she should have waited for the district nurse.
The district nurse then told the practice, which called in the daughter, concluded "that the doctor-patient relationship with the family had broken down", and struck all three off.
When she asked why no warning had been given, the practice merely replied that staff did not wish "to go into specific details".
The daughter complained to the Ombudsman, saying she felt "totally devastated and distressed" at her family's treatment by the practice. Their mother, she added, died a few weeks later "totally distraught" at their collective removal.
The complaint was upheld and practice staff apologised.
In another case, an elderly man wrote asking for an apology from a practice manager, following a verbal disagreement between the official and the man's wife over unanswered calls to the surgery. The couple had been trying to fix appointments for flu jabs.
Instead, the practice manager told the woman: "I'll get you struck off for this."
She then received a letter from her GP alleging she had been abusive and used strong language that had "intimidated" and "humiliated" staff.
The GP said the practice manager had asked that the couple be removed, but she could remedy the situation by apologising to the man.
She wrote back, "shocked and horrified", saying: "Never before have I had a cross word with anyone in your practice."
She refused to apologise - and the manager subsequently sent her a letter informing her she was being removed.
In her submission to the Ombudsman she said she had "been made to feel like a criminal" and that Stockport Primary Care Trust, which officially removed her, had simply sided with the practice.
The Ombudsman upheld the complaint, ordering the surgery to put in new procedures and pay the couple £750 compensation.
The Ombudsman upheld all 10 complaints about de-registration that it investigated in the past year.
Ann Abraham, the outgoing Ombudsman, writes in today's report: "In a small but increasing number of cases, a failure to resolve disagreements between patients and their GP has led to their removal from the GP's patient list – often without the required warning or the opportunity for both sides to talk about what happened."
The review warned: "Decisions to remove a patient from their GP's list can be unfair and disproportionate and can leave entire families without access to primary healthcare services following an incident with one individual."
While dealing with aggressive behaviour was "not easy for frontline staff", the review found that some GPs "have applied zero tolerance policies without listening to and understanding their patients or considering individual circumstances".
Ms Abraham said that, overall, progress towards getting the NHS to "listen harder and learn more" from complaints - her call in last year's report - had been "patchy and slow".
"Knee-jerk responses by NHS staff" meant "minor disputes" often ended up with the Ombudsman, she said.
Nonetheless, she said there was now "a growing recognition that patient feedback is a valuable resource for the NHS", which did not exist when she was appointed in 2002.
A Department of Health spokesman said: "We expect all GP practices to follow the terms of their contracts and warn patients if they intend to remove them from their practice list."
Have you had cause for complaint at your doctor's?
Are you nervous of being struck off a GP's list?