The Care Quality Commission found three-quarters of the 79 hospital trusts visited under its new inspection regime so far had safety problems.
Over 40% of care and nursing homes and home care services and one in three GP services also had problems with safety.
Lack of staff - in terms of skills and numbers - was identified as a major issue.
The way medicines were managed and how mistakes were investigated and learnt from were also highlighted.
Among the individual cases flagged up were:
The findings - contained in the CQC's annual report - are effectively a mid-term update of the new tougher Ofsted-style inspection regime.
They cover the first 14 months of the inspection programme, which was launched in April 2014 and is expected to be largely completed by April 2016.
So far more than 5,000 organisations have been inspected - nearly half of hospitals, 17% of care services and 11% of GP surgeries and out-of-hours providers.
However, those deemed most at risk have been predominantly targeted first, so the level of failure is not necessarily representative of the overall sector.
5,439
organisations inspected
14 months
into 24-month inspection programme
47% of hospitals inspected
17% of social care services
11% of GP services
During the inspections, CQC experts look at a range of different issues, including the quality of management, whether staff are caring and safety.
Each organisation - from GP surgery to hospital - gets a rating for each, resulting in an overall rating of inadequate, requires improvement, good or outstanding.
The results of these are widely published throughout the year, whereas this report looks at some of the common problems identified during the whole process.
Of all the issues looked at, the CQC said most concerns had been raised about safety.
Some 13% of hospitals were judged unsafe, 10% of social care services and 6% of GP services.
Once those judged to be not safe enough are included, it brings the numbers with safety problems to 74% for hospitals, 43% for social care services and 31% for GPs.
The report said improving leadership was the key to tackling the problems.
David Behan, CQC chief executive, told Radio 4's Today programme: "What we know from our report and from other research is that the leadership of an organisation sets the culture of that organisation.
"If the leadership says the important things around here are quality and safety, then that's what people attend to."
Royal College of Nursing general secretary Janet Davies believes financial problems are a major factor - last week it was revealed trusts had already racked up a deficit of nearly £1bn in the first three months of this financial year, greater than the overspend for the whole of 2014-15.
She added nursing care, whether in hospitals, care homes or the community, depended on having the right number of staff with the right skills and support.
She added: "There must be more investment in training nurses, keeping nurses and listening to nurses."
Katherine Rake, chief executive of Healthwatch England, the patient watchdog, said it was vital to learn from mistakes, describing the problems highlighted as "unacceptable".
"We would now like to see all services operate with the right culture of openness and transparency when things go wrong," she said.
But Rob Webster, of the NHS Confederation, which represents trusts, warned the financial pressures and negative publicity was creating a "toxic environment", which in turn had caused a "revolving door of NHS leadership".
"[This] is bad for the health service, and bad for patients," he said.
Safety across the NHS and care sectors in England is a "significant concern", with particular problems in hospitals, inspectors are warning.