The CQC's State of Care report for 2017/18 acknowledged that practices received the ratings 'despite continuing pressures from a growing demand and high workload for staff'.
Less than 4% of practices were rated 'requires improvement', and less than 1% were rated 'inadequate', the report says.
Ratings for GP practices are significantly better than those for hospital services - where just two thirds were rated good or outstanding, with 31% rated 'requires improvement' and a further 3% 'inadequate'.
Although general practice has increased extended access substantially, with 41% of practices responding to an NHS England poll earlier this year saying they offered 'full provision outside of core contractual hours', the report says 'the general practice workforce is stretched'.
It warns that rising workload and falling numbers of GPs 'may be affecting people's access to their GP practice'.
The CQC report highlights the need for more collaborative working across NHS services to improve patients' experience of care. It says that a 'growing number of GP services are now working in multidisciplinary, multiagency ways'.
The report found that 'primary healthcare is changing in response to well-documented continuing challenges: a rising demand for services from a growing and ageing population with more complex health needs. This results in a higher workload and less sustainable work-life balance for GPs and other health and care staff, which then affects the sector’s ability to recruit staff'.
It warned that workforce shortages in primary care meant that some services were struggling to meet demand, with 'almost all' urgent care providers facing difficulties in filling rotas.
BMA chair Dr Chaand Nagpaul said: 'It is a testament to hardworking doctors and their colleagues that the NHS has managed to maintain high standards of care overall, despite the ongoing pressures of rising demand, workforce shortages and chronic under-resourcing.
'In particular, it is encouraging to see such a high proportion of GP practices performing so well and improving on last year’s figures at a time when the profession faces its own unique struggles.
'However, it is clearly worrying when almost half of A&E departments are rated as requiring improvement or inadequate, and more than a third of mental health trusts are not meeting safety targets.
'The CQC recognises the need for a joined-up health service, but it must also call for greater investment and infrastructure in the NHS if patients are to receive access to care when they need it most.
'Next month, the government will unveil its long-term plan for the NHS, and this must address the core resource needs of GP practices and hospitals to ensure patients are confident that the care they receive will be safe, of high quality, timely and easily accessible, regardless of where they live in the country.'