The fit note is not reducing absence yet as sickness time off increased to 190 million lost working days at a cost of £17bn to employers last year, the Confederation of British Industry (CBI) has said.
Its Absence and Workplace Health Survey conducted with Pfizer revealed that employers were disappointed with the early results of the initiative.
Despite introducing the fit note in 2010, the rate of absence was marginally higher than in 2009, when employees averaged 6.4 sick days, the lowest rate since the survey began in 1987.
Over £2.7bn of the £17bn bill is generated by 30.4 million days of non-genuine sickness absence.
This figure, it added, does not include other indirect costs such as lower customer service and lost productivity.
Despite strong support for the initiative, employers have been disappointed by their experience so far.
Two thirds (66%) of firms said that it had not yet helped their rehabilitation policy, and 71% were not confident that GPs were using the fit note differently from the old sick note.
The research also found that long-term absence accounts for nearly a third (32%) of all time lost to sickness.
In the public sector, the proportion is even higher, with long-term health problems causing nearly half (47%) of days lost, whereas in the private sector long-term absence accounts for 27%.
Mental health issues are the single biggest cause of long-term absence, followed by musculoskeletal disorders, back pain and cancer treatment.
Employees in the public sector took more sick days (8.1 per year) than those in the private sector (5.9), although this represents an improvement on last year's average of 8.3 days.
It suggested that reducing public sector long-term absence to near that of the private sector will be key to reaching overall private sector levels.
The CBI estimated that if the public sector could reach private sector absence levels, it would save the taxpayer around £5bn by 2015-16.
Katja Hall, chief policy director at the CBI, said: "The substantial costs of absence to the economy put a premium on managing longer-term absence well.
"The fit note is a great initiative, which could play an important role in helping people back to work and stopping them slide into long-term absence. But employers are far from convinced that the scheme is working properly and don't think GPs are getting the necessary training.
"The launch of the electronic fit note should be an ideal opportunity for the Department of Work and Pensions to extend the reach of its training programme and address GPs' engagement.
"There can be no room for complacency in addressing the so-called sick note culture," she added.
