BAE sold Tornado and Hawk jets to Saudi Arabia under the deal
The Serious Fraud Office's conviction rate has dropped from 82% to 61% in five years, a report has found.
The report published by the Attorney General's office was from Jessica De Grazia, a former prosecutor in the US.
The report said the SFO had lower conviction rates and used more resources than its US counterpart.
The new director of the SFO, Richard Alderman, told the BBC that "there was a lot more we can do to protect the public" from fraudsters.
The report blamed a shortage of skills at the SFO, a lack of investigative support from the police and cumbersome disclosure rules.
Mr Alderman told BBC Radio 4's PM programme that the SFO planned to invest heavily in training.
The SFO came under scrutiny earlier this year after the High Court ruled it was unlawful to end an investigation into a £43bn BAE arms deal with Saudi Arabia.
Defence firm BAE was accused of making illegal payments to Saudi officials to secure contracts, but the firm maintains that it acted lawfully.
The SFO said national security would have been undermined by the inquiry.
Mr Alderman said the House of Lords would now decide whether the SFO had acted unlawfully after it was granted leave to appeal the ruling.