Mr Cocks said staff were aiming for the clinic to be up and running by Monday for all patients, although not at full capacity.
"We see around 500 patients a day so it is vital."
He said alternative locations for a more suitable clinic could be opened in the next two to three weeks. Staff had been working tirelessly to get things back to normal. "We are making good progress."
Businesses attached to the building were not damaged in the fire.
The pharmacy is now open and Medlab was shifted to the hospital but is hoping to return to the building soon. The Medtech system is operational and prescriptions can be ordered. Masterton Medical serves 23,000 patients and is the largest of its kind in NZ.