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"We take full accountability... We can go back in the history of when this project started, how Eskom was on the back foot. We have continued to be on (the) back foot for most of this project," he said in an interview with SAfm.
On Monday, Eskom said in a statement that the new power station would probably only begin contributing to the national grid in the second half of next year. The previous target was December this year.
"I think we said from the beginning of the year that we had been highlighting some technical problems with the boiler and the welds and we also highlighted that the control and instrumentation system, at that stage, had failed," O'Flaherty said.
The boiler problems related to inadequate post-weld heat treatment, and the replacement of welds which were made using unqualified procedures.
This was not the first delay because of welding problems. Previously, faults in factory welds had been discovered.
O'Flaherty said that 9 000 welds needed to be tested, as Eskom "would never ever sacrifice safety" and this process had not yet been completed.
The construction delays have been partially blamed on contractor Hitachi's failure to deliver top quality boilers at the plant.
In May, Public Enterprises Minister Malusi Gigaba said strong measures were taken against Hitachi for its sub-standard work on the Limpopo power station.
O'Flaherty said: "A lot of commentators are saying Eskom must control the contractors better, and that may or may not be true.
"We paid contractors a lot of money to perform and we have not had that done."
He said Eskom was entitled to recoup some of the funds back from contractors.
"We will follow the contracts. The contracts are quite clear in that contractors who cause delays and who cause cost overruns - we are entitled to claim some of those costs back."
Eskom was busy working out its strategy in this regard.
Asked whether this would be the case for Hitachi, O'Flaherty said he would not be drawn into a commercial debate.
Hitachi Power Africa is 25% owned by the ruling African National Congress' investment arm, Chancellor House.
"Certainly, we have to look at all of the contractors and they [Hitachi] would be one of them."
Labour problems have also dogged the construction project, with no work being done on the site between January and April.
In March, Gigaba intervened and said the construction deadline would not change. He said strict penalties would be imposed on contractors should they fail to meet their obligations.
