Incorrect results can mean clinical staff fail to spot how unwell a patient with respiratory problems is becoming, they said.
According to the study, published in the journal ERJ Open Research, this widely used method, which counts breaths over a 30-second period, fails to take account of people's irregular breathing patterns.
"The lack of accuracy in measurement of respiration rate could have an impact on a patient's treatment," said study author Gordon Drummond from the University of Edinburgh in the UK.
"We think accuracy would be improved by increasing the time of measurement to two minutes and using specialist equipment to measure respiratory rate," Drummond added.
For the findings, the research team focused on what is referred to as the respiratory rate, which is the measurement of the number of breaths a person takes in one minute.
The rate is measured in all patients who arrive in hospital feeling unwell, as part of what is known as a warning score chart.
Most clinical staff believe that counting breaths taken over a 30-second period will give a reasonable measure of the respiratory rate, the researchers say.
As breathing is not always regular, however, there can be a variation in the respiratory rate when measuring it over a short time period.
The team analysed recordings of breathing in 25 hospital patients to determine how wide this variation can be.
Each recording was made for between 30 minutes and an hour in patients with illnesses that included respiratory, cardiac, neurological and urinary conditions.
Researchers sampled the recordings at random, many times, in the same way the clinical staff might measure the breathing rate.
It was found that there was a large variation in the respiration rate for each patient - more than half of the measurements differed by more than three breaths per minute.
"This change may sound small but, in 40 per cent of cases, the incorrect rate would have meant the warning score chart was wrong," the researchers stressed.
The practice - key to assessing risk in many Covid-19 cases - could be improved by increasing the time of measurement to two minutes, the study noted.