Some of the overspending was because of poor billing by Telecom where charges had been duplicated or charged to the Otago board instead of Southland.
Also, the increasing amount of data going over the internet was affecting the amount spent.
Hospital advisory committee chairman Richard Thomson said this had been going on for some months and there was frustration at the time it was taking to resolve.
Speaking after the meeting, Mr Mackway-Jones said about half the cost related to increased sending of digital images between hospitals.
Regional chief information officer Grant Taylor said these increased costs were not a bad thing and resulted in improvements to patient care.
For instance, clinicians now had the ability to send images to get second opinions from specialists elsewhere, particularly where there might be a sole specialist available in Dunedin.
Clinicians were also accessing up-to-date information from websites.
As technology was upgraded it was not always easy to anticipate the amount it would be used; hence the increased costs.
Information technology leases are also over budget by $192,000 for the year so far, Mr Mackway-Jones told the board.
This was because delays in some projects - including the new patient administration system originally planned for last November - meant leases involving old systems had to be extended.
