At Wednesday's Senate estimates hearing, Defence department's deputy secretary for the capability acquisition and sustainment group (CASG) Kim Gillis said he spoke with BAE Systems' CEO about the loss of the manual which was on a single CD.
"He gave me some context about what actually happened ... how they are changing their processes," Gillis told the Senate estimates hearing in Canberra on Wednesday.
"We take any loss or any security breach seriously."
Gillis added that the Department of Defence would not be reviewing any contracts with BAE Systems following the incident, noting it occurred outside of the company's defence sector dealings with the Commonwealth.
The security manual remains missing and parliamentary officials were not told about it until three months after it was lost.
The Senate estimates hearing on Monday was reassured that around half the manual comprised publicly available material, while other parts were redundant or had been modified in recent months.
A statement from BAE Systems Australia said, "Following identification of the security incident, we conducted a thorough investigation and are confident that we have the processes and procedures in place to avoid the possibility of an incident of this nature happening in the future.
"We also understand that there has been no compromise to the security of Parliament House."
The Department of Parliamentary Services conducted an independent review of the incident, with BAE Systems required “to reassess its document-handling procedures”.
BAE Systems Australia is competing for the $5 billion LAND 400 Phase 2 Project and Project AIR 2025 Phase 6 Jindalee Operational Radar Network.
BAE Systems (UK) is also bidding for the $35 billion Future Frigate Project against Spain's Navantia and Italy's Fincantieri.