A senior Ministry of Defence (MoD) official has recommended sending the jobs to Bristol, despite an internal report finding that staying in Glasgow was the cheapest option.
SNP Westminster leader and defence spokesman Angus Robertson condemned the move.
The MoD has slashed thousands of jobs since 2010 as part of the Government's bid to trim the public sector.
The Sunday Herald can reveal that the UK Nato Codification Bureau (UKNCB), which is funded by the ministry, is now facing major changes.
The division, which was transferred to Glasgow in the 1980s, catalogues equipment and hardware for the armed forces and Nato.
It codifies all component parts for items such as jet fighters, Challenge tanks and radars, and assists with export sales.
However, an internal review has backed relocating the bureau to the MoD site at Abbey Wood, in Filton.
If approved, the move could result in the loss of nearly 50 posts from Glasgow.
The relocation is likely to prove controversial as the review's executive summary listed a number of risks associated with the shift.
The report flagged up a potential "cumulative loss and dilution of skills and expertise", as well as a "loss of efficiency and effectiveness".
It also noted: "The cheapest costed option in any of the comparable timescales is for UKNCB staff to remain in Glasgow."
The report added: "A simple comparison between the levels of benefits (Medium) and risks (High) provides the conclusion that the arguments weigh clearly in favour of the UKNCB remaining in Glasgow."
Trade unionists have also hit out at the secret plan.
Gerry Burns, chairman of the Public and Commercial Services Union's Scotland West branch, said: "This is nothing short of a scandal. The Value For Money study came down in favour of Glasgow as the preferred location, yet senior officials are still proposing to move these valuable jobs out of the city.
"This is all about internal MoD politics, yet dozens of members stand to lose their jobs and have their livelihoods ruined."
Alan Glover, the local Prospect Union representative, stated: "David Cameron and the other Unionist MPs are continually stating that Scotland benefits from being in the union, yet it seems here that Scottish jobs once again are being placed on the sacrificial altar with no financial or business reasoning."
SNP defence spokesman Angus Robertson MP said: "It's shocking that such a decision can be made despite evidence that Glasgow is the cheaper centre to run, and at a time when service and civilian defence jobs in Scotland have reached record lows.
"This is an unacceptable blow to the hard-working personnel running an efficient centre in Glasgow."
An MoD spokesman said: "The MoD remains committed to bringing down the national deficit by reducing costs and driving efficiency wherever possible.
"The MoD is considering the future size and shape of the MoD's UKNCB but no final decisions have been taken."