The UK agency said it lost 32,000 pages of data and 81 audio tapes linked to a bribery probe into BAE's al-Yamamah deal with Saudi Arabia.
The investigation into the huge arms deal was discontinued in 2006 after intervention from then-Prime Minister Tony Blair.
The SFO said the lost material comprised 3% of data about the deal.
It said it lost the items when it returned more material than intended to a source in the investigation.
The data loss took place between May and October 2012 and was discovered in May this year.
The SFO said it had contacted the 59 suppliers of data for the investigation to inform them of the situation.
"Any loss of data is a serious matter and the SFO has taken action to ensure no further material can be wrongly sent out," the agency said in a statement.
It continued: "The SFO has a duty to return material to those who supplied it, upon request, after the close of an investigation.
"In this instance the party requesting the return was sent additional material which had in fact been obtained from other sources."
Peter Mason, former director of security at the Palace of Westminster, has conducted a review and made some recommendations, including raising the profile of data handling as a key risk in the SFO's business.
A former civil servant, Alan Woods, is also conducting a wider-ranging review of SFO processes.
The al-Yamaha deal involved the sale of tens of billions of pounds worth of arms by BAE Systems to Saudi Arabia, beginning in the 1980s and ending in 2006 with the sale of 72 Typhoon fighter jets.
Allegations of corruption and bribery led to an SFO investigation in 2004, but it was closed in 2006 on grounds of public interest, amid concerns that relations with Saudi Arabia were being harmed.
The firm paid $450m (Â£289m) in fines in the UK and US three years ago to end other corruption investigations in both countries.
It pleaded guilty to one charge of conspiring to make false statements to the US government, including on deals in Saudi Arabia, and in the UK on one charge of breach of duty regarding payments made in Tanzania.
Speaking about the data loss, a BAE spokesman said: "Ultimately, this is a matter for the SFO and as far as BAE Systems is concerned, it is now closed."
Labour MP Emily Thornberry, shadow attorney general, said the incident "raises more questions than it answers" and asked what the government was doing to "ensure that this never happens again".

American Woods, 40, has not played tournament golf in almost a year and had two operations last autumn in an attempt to cure a back problem.
His agent has confirmed he will not play for the rest of this season as he is not ready for "competitive golf".
The 14-time major winner has dropped to a world ranking of 628.
We've launched a new BBC Sport newsletter, bringing all the best stories, features and video right to your inbox. You can sign up here.
The Serious Fraud Office (SFO) says it has lost thousands of documents relating to a probe into BAE Systems.
[NEXT_CONCEPT]
Tiger Woods has withdrawn from the US PGA, meaning he will miss all four majors in a calendar year for the first time since his Masters debut in 1995.