The system has been running with no reported problems since 9am, ELGA boss Susanne Herbek said on Wednesday.
The plan is to gradually roll out ELGA so that by the end of 2017 all its encrypted information can be accessed by all hospitals, pharmacies and doctors across Austria, as well as the patients themselves.
Austria's Health Minister, Sabine Oberhauser, has dismissed critics' concerns about patient privacy and the security of the system, saying that access to the encrypted data is subject to the tightest restrictions and the express permission of the patient.
Abuse of the system could result both in fines and criminal charges.
People can choose to opt out of the scheme, and so far 226,000 have done so.
The Austrian Association of General Practitioners (Österreichische Hausärzteverband) is critical of the scheme, saying that it is not yet ready to be used with real data and that “there is a huge mismatch between possible gain and the real costs and brain power required".