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Whitestone Family Practice in Ribble St was burgled on Wednesday night, almost three weeks to the day since police believe controlled drugs were targeted in a similar burglary on August 1.
A forensic examination was carried out at the scene yesterday.
Staff members reported the break-in to police after arriving at work yesterday morning.
Sergeant Blair Wilkinson, of Oamaru, said police were working to establish exactly what had been taken.
"Generally, when medical premises are targeted it's prescription pads and controlled drugs that are targeted."
Whether the burglaries were linked was yet to be established.
"Both burglaries have been investigated together, but we are keeping an open mind as to if it's the same offender or offenders. A line of inquiry is being followed."
In an effort to support medical centre staff in Oamaru, police visited several practices yesterday, he said.
"We've gone around all of the local doctors and talked to them about their security and looked for ways we can help prevent them from further offending of this nature."
Inquiries are continuing.