"We believe that's the way to best protect the reputation of CSIRO," he said.
The shadow minister for science, Sophie Mirabella, criticised the government for failing to conduct an independent enquiry.
"Months after the government was embarrassed into launching an investigation into these very serious allegations of corruption at CSIRO, we hear today that the investigation is being conducted by none other than CSIRO itself," said Mrs Mirabella.
"CSIRO should have nothing to fear from a genuinely independent investigation into allegations of serious misconduct," she said.
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