But Mr Cocks was quick to reassure patients no medical data on anyone had been stored on the laptops.
"That has not been compromised and we can put people's minds at rest, as all that information is stored with a centralised service," he said.
The stolen prescription pads contained prescriptions for controlled drugs and, as a result, a general alert had gone out to all pharmacies to be on the lookout for anyone trying to obtain drugs by using them.
"We have also notified the Ministry of Health," Mr Cocks said.
In the aftermath of Saturday night's break-in, security guards had been hired to keep an overnight watch on the premises on Sunday.
"But unfortunately we didn't extend that to Monday night and that's when they returned - it was all rather brazen."
Focus, the next-door business that is essentially a needs-assessment service for older people and the disabled, lost computers and a full emergency-preparedness kit.
Mr Cocks said much of the stolen equipment would be useless to anyone who was not a doctor.
He said the computers alone would be worth well over $10,000 because many were near-new, having been bought as replacements for those lost in a fire that partly gutted the former medical premises in Lincoln Rd.
Mr Cocks said it was not the value of the equipment taken but more the attack on a medical facility serving the district that was distressing.
"This sort of thing should never happen, it's really disappointing."
On the upside was the fact the old hospital premises where Masterton Medical was now housed had security cameras in place. It was hoped images captured on film could lead to those responsible.
Mr Cocks said police had been alerted to the burglaries, and a forensic team had carried out tests.
