The St Athan centre would be a major source of military training
The planned switch of military training to Wales to set up a £11bn new facility could be put back eight years, an e-mail obtained by BBC Wales suggests.
Building on the centre at St Athan in the Vale of Glamorgan is due to start next year, bringing 5,000 new jobs.
The Ministry of Defence (MoD) said it remained "100% committed" and there was "no question" about its future.
Metrix, the consortium backing the operation, said the transfer was just one detail of a "complex" project.
The memo leaked to BBC Wales' Dragon's Eye programme stated the Metrix consortium was considering keeping open HMS Sultan in Hampshire.
The training college at Gosport, at the mouth of Portsmouth Harbour, is the home of a number of organisations, including Royal Naval Air Engineering and Survival School.
It was due to close and move its training to south Wales in 2017, but the leaked e-mail said it could stay open until 2025.
Union leaders fighting to keep work in Hampshire say the leaked e-mail raised questions about the proposals.
The PCS union opposes the plan to transfer. Paul Bemrose, a negotiations officer with the union, said the e-mail offered his members a degree of comfort.
He said: "There are a lot of problems with the programme now in terms of affordability, which the MoD are not talking about, because they don't want to raise the spectre of the project collapsing."
However, Metrix said the transfer of HMS Sultan was only one part of a scheme involving thousands of jobs.
The firm said details were bound to change in what it described as a hugely complex programme running over 25 years.
The MoD said: "There is no question whatsoever about the future of this project, which will bring world class training to our armed forces".