But performance in sports which received Lottery money was "mixed", with six Olympic disciplines - gymnastics, judo, triathlon, shooting, taekwondo and weight-lifting - delivering no medals despite receiving £12.4m in funding between them.
Four Paralympic sports - wheelchair rugby, sailing, boccia and wheelchair fencing - produced no medals despite £1.3m funding from the programme.
Concentrating Lottery funding on sports with a track record of success could help Britain build on the victories of stars such as Kelly Holmes and avoid flops such as swimming's world 200m backstroke champion Katy Sexton, who finished seventh despite being hotly tipped for gold.
The report adds that UK Sport should consider reducing the number of athletes funded by the WCPP, focusing on fewer sports, or even introducing performance bonuses for medal-winners.
"There is scope for UK Sport to improve management of the funding programme," said the NAO.
"UK Sport should be prepared to take tough decisions based on performance about which sports merit funding and on what scale."
UK Sport is shortly due to agree individual funding packages for the four years of preparation for Beijing. Resources from the WCPP are already focused on the "priority" Olympic disciplines of athletics, cycling, rowing and sailing, which received 55 per cent of the money in the run-up to Athens and delivered 61 per cent of the medals - including eight of Britain's nine golds.
Acting chief executive Liz Nicholl said UK Sport have already drawn up a performance investment strategy to ensure that "funding is targeted at those athletes who have a realistic chance of making the podium in 2008, with more resources being available for fewer athletes".
"Our task is to make sure that we build on the success of Athens and continue to sharpen our focus, in order that we can enjoy more medal success in Beijing," she said.
"There is no doubt that the advent of Lottery funding has enabled us to take the package of support we can offer to our leading sports to a new level, as the results from Sydney and Athens clearly demonstrate.
"But British sport will collectively have to up its game again to improve in Beijing and UK Sport must play its part in full."