Council engineering, hazards and science director Gavin Palmer said the work was undertaken between mid-morning and early afternoon on Saturday.
Gravel-filled bags and other rock work had reduced the backflow that had threatened to undermine the pumping station on the Taieri River stopbanks, near Allanton, he said.
A 75m-long series of bottom-hinged metal flap-gates had been opened on Friday, as part of the design of the Lower Taieri Flood Protection Scheme.
The aim of opening the gates was to increase the flow of water into the protective upper ponding area, and reduce the flow in the Lower Taieri River downstream of this point.
Flood control checking and remedial work would continue, Dr Palmer said.
Although a deterioration in weather conditions had been predicted for later in the week, he believed this would not threaten the stopbanks near the pumping station.
Neither the repaired stopbank damage nor the folding down of the flood control flap-gates would adversely affect continuing flood control preparations, he said.
