He said the software was provided to them by the Information Technology department, which had procured it from a private firm.
The error led to exorbitant power bills and in some cases showed zero bill amount.
"We are totally unhappy with the services of the company which has provided the software," Sequeira said.
The power department is perturbed as the software company and Information technology department officials have refused to co-operate with them on rectifying the issue.
"We are sorry for the inconvenience caused to consumers," the minister said adding the department will now opt for on- the-spot billing.
Sequeira said the department has introduced on the spot billing in his own constituency at Loutolim and it will be soon introduced in rest of the state.
"There will be no billing arrears and faults once bills are generated on-the-spot," he said.