Having experienced life as a junior doctor, much of the criticism I have read about the NHS is well placed. But I was surprised to find myself thinking that last week's bad press, which painted a picture of our services as a useless machine into which endless money is being poured while it churns out results of ever-dwindling productivity, was a bit too harsh.

The Times, among others, condemned spending on the NHS as a waste because its productivity has declined. These news stories follow the recent results from the Office of National Statistics showing that between 1995 and 2008 the amount spent on healthcare rose by 75%, or an average 4.4% a year, but the amount of healthcare provided rose by only 69%, or 4.1% a year. This means that the productivity of publicly funded healthcare fell by an average 0.3% every year from 1995 to 2008.

There is no denying that there is waste in the NHS, but we could be overestimating just how much waste is occurring, because NHS output is currently being measured by "productivity" which does not come close to capturing what the NHS is actually achieving.

Although much money has been soaked up by bureaucracy, this time a fair amount of the resources did get to the front line: money was spent on increasing the number of clinical staff working for the NHS (89,000 more nurses and 44,000 more doctors). Critics will say that the increase in the numbers of patients treated shies in comparison to the vast amount of services bought by the NHS. This is a valid point, but a higher staff to patient ratio is not necessarily a waste. In my experience this is precisely what patients ask for on a daily basis.

I have also worked in well-staffed and badly staffed departments, and witnessed how better staffing makes the NHS a safer place. Fewer patients allocated to each nurse means nurses can detect and assist unstable patients faster. A hospital in which there is always a senior doctor available to supervise a junior doctor who is performing a new procedure has a very different atmosphere from one in which the junior is left to get on with it and try their best. When the statistics are analysed, the first hospital will show up as less productive as two doctors are effectively "being used up" on one patient, but I know which hospital I'd rather be in.

An improvement in NHS safety records in recent years is backed up by data from the National Patient Safety Agency. The risks of dying or suffering serious harm at the hands of the NHS as a result of an accident or mistake have fallen sharply. Latest figures show a 37% fall in the number of deaths following accidents or mistakes, and a 34% fall in incidents causing serious harm between 2008 and 2009.

Thinking about issues like patient safety reiterates the fact that the NHS isn't a business and that output cannot be measured in simplistic terms of productivity. We need to measure the quality of service that is being provided. Although the ONS has recognised quality as an important factor and tried to incorporate it when measuring NHS output by putting a value on any increase in short-term survival rates, shorter waiting times and primary care performance indicators such as improvements in blood pressure, it itself admits that measuring quality in the NHS is very difficult. There are still significant aspects of quality that the data fails to capture, such as patient safety. Plus the current method of looking at NHS output does not adequately correlate with what patients want. For example, patients may want longer consultations with their GPs, which may be very beneficial for a patient in terms of long-term health outcomes but using the current model would yield a low output and be deemed a negative outcome.

In a machine as big and clumsy as the NHS, waste will always be a very real threat. But perhaps we should consider the possibility that the NHS is doing a great deal more for its patients than ever before. To know what the true situation is, we need to think about what patients want from their NHS and find a way of measuring NHS output that reflects whether this is being delivered.

• This article was commissioned after the author contacted us via a You tell us thread