"Certificates may have financial implications for the patient through benefits, employment and compensation payments, and failure to complete a certificate or including certain information may have a negative impact on the patient or the patient's family."
Doctors were also restricted in how much information they could provide to an employer, insurer or government agency, the council said.
"They may only provide the information that is required by the agency, and which the patient consents to being released. This can create difficulties when the third-party has access to some, but not all, of the relevant information."
First Union general secretary Robert Reid said it was a further erosion to worker rights.
There was also an issue with doctor-patient confidentiality and the doctor being put under pressure to release details of their patient's condition.
"I am disturbed that it looks like doctors are really being leant on by forces outside of the relationship that they have with their patients to breach more and more of the confidentiality between patient and doctor."
He said arguments that it would be harder for workers to take sickies held no weight, because in today's economic climate workers were predominantly industrious.
"I really get angry with those sorts of statements from employers who essentially make out workers to be malingerers, and therefore they're having to be checked on for every single thing they do."
Employment lawyer Max Whitehead said employers often knew instinctively when an absence was "dodgy", but were powerless to contest it when a doctor signed a medical certificate.
"Rather than challenging a patient's honesty, doctors declare them as sick. This means the doctor gains financially and the powerless employer has to lose a day's work and pay a day's wages."
But Council of Trade Unions president Helen Kelly said any suggestion that doctors were faking certificates was "an absolute outrage".
"It's just not true," she said.
Employers and Manufacturers Association occupational health and safety manager Paul Jarvie said doctors should be able to focus on what people could do, rather than what they could not do.
"If the doctor is continuously signing someone off then that's going to raise questions with the employer about 'Well how long can I have this person not being at work because I've still got a business to run'."