The spending watchdog said in a statement on its website this month that it had begun an inquiry into the scheme, which offers 16 and 17-year-olds in England and Northern Ireland the opportunity to take part in residential activities and community work.
The government announced at the Autumn Statement last year that it would expand the NCS from 80,000 places a year to 300,000 by 2020, supported by £1.2bn of government funds, despite the fact that the scheme has consistently failed to hit its participation targets since it was launched in 2011. Almost 58,000 of the 80,000 places offered in 2014/15 were filled.
The NAO said its report would also examine early evidence on whether the programme was working, the challenges in meeting what the NAO said was "ambitious 2020 participation and growth targets", and whether the system was set up in a way that would support the level of continual growth required.
The report is expected to be published in January.
It comes as the House of Lords prepares to debate this afternoon the National Citizen Service Bill, which will put the scheme on a statutory footing and require it to report to parliament on its plans every year.
Peers due to speak in the debate include the Conservative peers Lord Hodgson of Astley Abbotts and Lord Wei, the government's former big society adviser, and the Liberal Democrat peer Baroness Barker.