The Department for Digital, Culture, Media & Sport has revealed that it received a second complaint about the National Citizen Service Trust from another organisation involved in delivering the young people's scheme.
The trust, which is the charity that runs the National Citizen Service, is already being investigated by the DCMS after receiving a complaint from The Challenge, which is the largest provider of the scheme.
A spokesman for the DCMS, which awarded the trust £185.7m in 2017/18, told Third Sector: "We have received a separate complaint from a small NCS delivery partner in relation to future NCS contracts.
"We will not provide an ongoing commentary while the issues are being explored."
The Challenge is suing the trust for £22m, the majority of which relates to alleged deficiencies in the trust's IT system.
John Kerslake, chief operations officer at the trust, said: "The NCS Trust would like to make it absolutely clear that the DCMS has received a complaint from a delivery partner that is wholly separate and unrelated to the legal proceedings involving The Challenge.
"When a commissioning authority undertakes its role, not everyone is always happy.
"We have seen the complaint, we are discussing this with the delivery partner and its managing partner, and we are seeking to address any issues, which we always do when we receive a complaint."
The Challenge wrote to the DCMS on 15 July outlining its concerns about the trust.
Shortly afterwards the trust withdrew The Challenge's preferred-bidder status for the next round of NCS contracts, which begin at the start of next year.
The trust said this was because the two parties were unable to agree on a contractual requirement to use the trust's shared IT system.
A spokeswoman for The Challenge said: "Our complaint is not linked to that of any other organisation, although we are aware of extensive concerns across the NCS network.
"We look forward to working with the DCMS to resolve the issues we have raised."
More than 400 staff at The Challenge face uncertain futures when its current contracts expire at the end of the year.