Polyclinics may damage trust between the patient and GP, harming the quality of care in the process, experts say.
A Leicester University study quizzed 236 patients about continuity of care - seeing the same doctor on each visit.
The researchers found those who saw the same GP were more likely to trust them and keep to courses of medicine.
But the government denied the network of super clinics being set up in England would cause disruption to the GP-patient relationship.
Polyclinics are large health centres housing a range of health professionals such as GPs, nurses, physiotherapists and hospital doctors.
"Our overriding objective is to deliver the best possible service to patients"
NHS bosses have been told to set up 150 centres outside London, while a host of them are expected to be created in the capital.
They have been designed to relieve the pressure on hospitals by providing a whole range of basic care.
Doctors' leaders have been critical, saying they will put the traditional system of GP care under threat.
The researchers surveyed patients from three GP practices asking them to give marks for the trust they felt in the doctor they had seen during their last visit.
A total of 150 had seen their usual GP with the rest seeing a different one.
In-depth discussions were also carried out with 20 patients and 12 GPs.
Those seeing their usual GP gave them a trust rating of 83.5 out of 100, while those seeing a different one gave them 72.6.
Having good care in the past and the expectation that the GP would provide the follow-up care in the future were cited as the main reasons for the usual GP scoring highly.
Patient trust
Lead researcher Carolyn Tarrant said the findings had major implications for government policy as polyclinics and other large health centres were likely to have large numbers of GPs.
"If patient trust declines, then medical outcomes may be adversely affected"
"The government is setting up numerous polyclinics, super-surgeries and walk-in centres all over the country.
"They are bound to reduce continuity of care and our research show that this may lead to a decline in patient trust.
"If patient trust declines, then medical outcomes may be adversely affected."
She said this could include failure to follow prescriptions or advice from doctors.
Dr Laurence Buckman, chairman of the BMA's GP Committee, said: "For someone with a chronic condition, a long-term relationship with a doctor they trust and who knows their history is vital."
But a Department of Health spokesman said the network of health centres was on top of existing GP services, not instead of them.
And he added: "Our overriding objective is to deliver the best possible service to patients.
"Patients repeatedly tell us that they want better access to GP services and want healthcare that is more personalised and convenient, so services need to adapt to respond to this need."
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