The Commerce Commission says it has received a complaint from two feuding health providers and will assess its worth to see if a full investigation is needed.
Relations have broken down between Medtech Global, which provides software systems for GPs practices, and Healthlink Ltd, which provides software to send information between practices when patients change GPs.
Healthlink says Medtech's proposals would add $4 million to $8 million a year to the health budget.
Medtech disputes this and says it will cooperate with the Commerce Commission.
Medical Association chair Peter Foley says good computer systems are vital for GPs to work effectively.
Dr Foley says he does not understand the full details of the dispute, but stresses he would be concerned if there was an increase in costs to doctors, when they have already invested heavily in computer software.