"It is not factually correct to say that serving officers will evaluate the performance of the ministers," the PMO said in a statement.
The statement said, "The Prime Minister's order is clear that the entire process has to be driven by the ministers."
According to earlier media reports, the government had developed a Performance Monitoring System (PMES) under which the performance of ministers "would be reported by bureaucrats".
The statement also said, "It is also not true that a minister and secretary are jointly required to sign the Results-Framework Document (RFD)."
"The PM's order does not have any such requirement. The minister has the prerogative and the final authority to decide on the priorities and deliverables for the concerned department at the beginning of the year," the statement added.