Medical clinics have been pocketing up to $50,000 a year in bonus payments to sign people up to the My Health Record scheme, amid concerns patients have been registered without their informed consent.

Thursday was the deadline for people to opt out of the scheme.

Doctors are eligible for payments of $6.50 a patient – capped at $12,500 a quarter – under the incentive program.

To receive the payments, healthcare providers must meet five requirements, including a target of uploading health summaries of some patients.

The former health minister Sussan Ley signed off on a rule in December 2015 stipulating that healthcare providers no longer needed to keep records of consent as part of the My Health Record “assisted registration” process.

Steve Hughes, a farmer from Macksville in northern New South Wales, said his medical clinic had conceded they had signed him up for a record without his consent.

He has since lodged a complaint with the Office of the Australian Information Commissioner, which told him it warranted further investigation. However, they will not be able to assign someone to look into the matter for four to five months.

“I’m very unimpressed. It’s an invasion of privacy,” Hughes told the Guardian.

“It shouldn’t happen [the payment incentives.] If the scheme is worthwhile, people will sign up.”

Fremantle writer Andrea Glazier said she had been trying to opt out of the scheme for the past five months and was told by call centre staff they could not help her out because she already had an account, which she did not know about.

She previously lived in Sydney and used a doctor at Warringah day surgery in Brookvale. The clinic has been contacted for comment about whether it received practice incentive program payments.

“I was a bit disconcerted,” Glazier told the Guardian.

Despite many calls to the hotline and multiple assurances that a confirmation letter would be sent out about the account being deleted, Glazier is still in the dark about her account’s status.

“It’s a fiasco really … it’s a suck of energy dealing with this,” she said.

A Melbourne man in his mid-30s, who did not want to be named, is also furious that his clinic created a record for him without his consent and might have profited from the exercise. He is a patient at the Chapel Gate Medical Centre.

“I was horrified, because it would never have been something that I would have consented to ever,” he told the Guardian.

The medical centre’s parent company, MAACG medical group, declined to say whether it received incentive payments for signing patients up to My Health Record.

Its managing director, Trish Wilson, said in a statement that the clinic “acts at all times in the best interests of doctors’ patients and with their informed consent”.

“Chapel Gate Medical Centre can not and would not comment about the treatment of an individual patient without that patient’s written consent,” she said.

She said the centre participated in the My Health Record program and adhered to all the legislative and professional standards.

The Privacy Foundation spokesman Bernard Robertson-Dunn said patients might see a conflict of interest with the incentive program.

“This issue has the potential to have a negative impact on the trust between the patient and their GP,” he said.

According to the Australian Digital Health Agency, there are 6,450,277 people enrolled in the My Health Record as of mid-January.

A spokesman for the agency said a healthcare provider “must seek a patient’s consent prior to registering them for My Health Record, otherwise they may be in breach of the Privacy Act 1988 (Cth)”.

“There are multiple steps in the registration workflow that require patient consent,” he said.

The agency was unable to say how many clinics were receiving incentive payments to sign people up for My Health Record or how much had been paid out to date.