The NAO found that while government funding covers £1,562 spending per participant in the social action programme, the actual cost for each of the 93,000 15- to 17-year-olds taking part during 2016 was £1,862.
To stay within budget, the NAO says costs need to fall by 29 per cent to £1,314 per young person by 2019.
A failure to meet participation targets was also highlighted as a major concern. In 2016, five of the nine providers "significantly missed" these targets and since 2010, none of the annual participation targets have been met.
If the current annual rate of increase is sustained, there would be only 213,000 participants in 2020/2021, significantly short of the 360,000 target for that year.
Providers told the NAO they were aware that they needed to invest more time in promotion through school assemblies and other direct contact, but "this created additional costs, which could outweigh the payments received".
Contracts with providers were on a payment-by-results basis to fill places, but the NAO found around £10m had been given to them for places that were not filled, although there are plans to recover these costs.
The contracts were also not explicit enough in incentivising providers to meet the aims of the NCS to boost social responsibility and engagement among young people.
NAO head Amyas Morse called on the Office for Civil Society (OCS) and NCS Trust - which manages the scheme - to "think radically about the aspects of the current programme that work and how best to achieve the NCS's aims at a more affordable cost to the taxpayer".
Despite concerns around funding and low take-up, the NAO acknowledged that young people taking part had been positive about their experience, with 84 per cent who were surveyed in 2015 saying they would recommend it to others.
Morse added: "NCS is now at a critical stage. The OCS and the trust have shown that NCS can attract large numbers of participants, and participation has a positive effect on young people. These are no small achievements, but it remains unclear whether these effects are enduring and whether NCS can grow to become 'a rite of passage' available to all 16- to 17-year-olds."
Meg Hillier, chair of the public accounts select committee, said: "With the National Citizen Service costing the public purse almost £2,000 per participant, and its ambitious growth targets having been repeatedly missed, it is difficult to see how it will be sustainable in the long term."
The government has committed £1.26bn of funding for the NCS up to 2020 and by 2015/16, £443m had already been spent.
A Department for Culture, Media and Sport spokesman said: "More than 300,000 young people have taken part in National Citizen Service so far, with the programme improving lives, strengthening communities and helping build a society that works for all.
"We want all young people to participate in social action and start a lifelong commitment to volunteering. The ambitious targets set have helped drive the rapid growth of the programme and we want to keep up this momentum and for the NCS to become a rite of passage for all young people.
"We are completely committed to ensuring value for money and will continue to work with the NCS Trust on this and the programme's continued expansion.
"The NCS Bill, before the House of Commons, will also further strengthen the governance and accountability of the NCS Trust. The government will carefully consider the findings of the NAO report and respond in due course."
Michael Lynas, chief executive of NCS, said: "The NAO credits the positive impact that the programme has on the young people who take part, which has been shown to endure in independent evaluations. The report notes that NCS has grown rapidly from 158 young people in 2009 to reach over 93,000 young people in 2016. The NAO draws attention to the diverse mix of backgrounds on NCS programmes with a higher proportion of people from disadvantaged backgrounds than the general population.
"NCS Trust is proud of these achievements which are a credit to the 300,000 young people who have had life changing experiences on NCS, and the network of hundreds of youth, charity and voluntary sector organisations that make the programme happen in communities up and down our country. While doing this, our network has reduced the cost of delivering the programme and we have remained inside our budget.
"We are grateful to the NAO for their recommendations, which will help us to strengthen our organisation so we can reach more young people, deepen our long-term impact and deliver even greater value for money."
The NCS - seen as a flagship initiative of former Prime Minister David Cameron - first launched in 2011. The aim is that eventually every teenager in England will get the chance to take part.