The Faslane nuclear submarine base on the Clyde, as well as the Coulport munitions depot on Loch Long, are protected by Ministry of Defence Police, which suffered cuts to their numbers in a Coalition Government announcement yesterday.
The attempt to save millions of pounds was denounced as a "kick in the teeth" by opposition MPs, who called for urgent reassurances over which sites would be affected, saying nuclear weapons stored in Scotland had to be properly protected.
The SNP also said concerns had been raised over the Coalition's decision to downgrade its assessment of the risk faced by some sensitive military sites ahead of the announcement.
The Herald reported last year that the Ministry of Defence Police – who are specialists in counter-terrorism – were facing damaging cutbacks, and that ministers were considering replacing those based at the Faslane naval base with military personnel trained to be "armed security guards".
Shadow Defence Secretary Jim Murphy said it was "essential" to know whether Faslane and Coulport were affected, along with munitions sites in Scotland.
He said: "There will be very real concerns about the impact on protecting munitions stores but most importantly our nuclear bases.
"We must be told the full implications of this decision."
He added that the cuts were a "kick in the teeth" for MoD Police.
Angus Robertson, the SNP's defence spokesman, described the cuts as "deeply concerning" and called for clarity on where they would fall.
He said that, while his party opposed the storing of nuclear weapons in Scotland, "they must be properly secured".
He added: "There has been concern that, ahead of this announcement, the MoD reduced their risk assessment at sensitive sites purely to justify cuts in police numbers."
Ministers announced that MoD police would see a reduction in their numbers of 700, taking them down from 3100 to 2400 by April 2016.
There will also be cuts in the MoD Guard Service, from just under 3300 members today to about 2200 by April 2015.
In a written ministerial statement, Defence Personnel Minister Andrew Robathan said regular service personnel would take a greater role in security along with local police forces.
Greater numbers of sites would be left unmanned, with only "physical security measures", he added, and suggested there could be more cuts to come.
The statement also warns that the changes, on which the Coalition plans to consult, will create "uncertainty and anxiety ... to the personnel involved".
The Defence Police Federation (DPF) accused the Government of putting savings ahead of safety.
DPF spokesman Eamon Keating said: "Ministers are happy to put the bottom line ahead of security.
"These decisions will put security of key establishments in the hands of security providers who lack the training, investigative powers and constabulary authority of MoD Police officers.
"The results will be greater risk to our establishments, assets and personnel, not less."