Only two of 570 bodies assessed, both of them hospitals, were ranked as excellent in both categories.
The Healthcare Commission said its "broad and tough" analysis showed the NHS needed to "raise its game".
The body representing NHS managers said underperforming trusts could now focus on areas where improvement was needed.
The "health check", which uses patient reports and hospital self-assessments as well as other financial and quality data to compile its rankings, replaces the discredited hotel-style "star ratings".
Factors assessed for the quality of service ranking included clinical care, meeting government targets and areas such as children's health, hospital acquired infection rates and community mental health care.
The financial management rating took into account both whether or not the NHS body had a deficit, but also how it ran its finances more generally.
The commission found 51% of trusts were ranked "fair" for quality of services, while 9% were ranked weak.
And 47% were ranked fair for financial management, with 37% deemed weak.
Eight hospitals were ranked as weak on both quality of service and financial management.
They, like other trusts given one weak rating, will have to have action plans in place setting out how they will improve within 30 days.
Primary care trusts, which commission health services for local areas, fared particularly badly in the analysis.
None of the 204 PCTs were ranked excellent for their financial management, while just 24 were ranked as good.
And just 93 were deemed to have good quality of service, while just six received the rating for their quality of service.
Trust re-organisation, plus increasing demands on community-based care, were cited as possible reasons for the findings.
Re-organisation was also cited as a major factor for no ambulance trusts being ranked as excellent for either quality of care or financial management.
'Things that matter'
Sir Ian Kennedy, chair of the Healthcare Commission, said: "Overall, the NHS must raise its game in some areas if it is to serve patients as they deserve.
He said patients would want a "universal guarantee" that trusts are meeting general standards - which covers areas such as safety and cleanliness.
"These are things that really matter to patients. We expect these standards will be met next year."
Health Secretary Patricia Hewitt said: "There is no doubt that the NHS has made big improvements particularly on waiting times, access to cancer treatment, community mental health services and treating patients with respect and dignity.
"But as these results show there needs to be even more improvement and we are working with the NHS to ensure that all organisations meet the core standards as soon as possible."
Shadow health secretary Andrew Lansley said: "It is a pretty sorry state of affairs when nine out of 10 primary care trusts have been rated only weak or fair.
"Even with an increase in resources, the government's policy of using PCTs to manage NHS resources is failing.
Liberal Democrat health spokesman Steve Webb said: "Patients will be horrified that so many hospitals are failing to achieve all of the basic standards in areas such as hygiene.
"Hospital managers should focus on getting the basics right, rather than being distracted by the latest headline-grabbing government initiatives."
But Nigel Edwards, director of policy at the NHS Confederation which represents over 90% of NHS organisations, said: "This move to a broader system is bound to uncover areas that need further improvement.
"All trusts will now be able to focus on areas needing improvement and will be working hard to improve standards of care."
He said the reorganisation experienced by primary care trusts and ambulance trusts had affected their performance.