Maritime unions said it was 'ominous' that HMS Ark Royal was used to supply the Portsmouth frigate HMS St Albans.
Normally the job is done by the RFA flotilla in its role as the navy's lifeline at sea.
But staff and unions fear it is a sign of things to come because of the £200m cuts to the defence budget called for in today's pre-budget report in Parliament.
As revealed by The News last month, shocked RFA staff were told in Portsmouth that the Treasury had pushed for cost savings that could mean the privatisation of the service.
A fleet auxiliary worker from Portsmouth, who does not want to be named, said: 'To have the navy showing how it can replenish ships without the RFA ahead of a major review is really insensitive. We are waiting to hear if we will be out of work and that seems like really bad timing.'
RMT spokesman Geoff Martin said: 'The display of a warship-to-warship replenishment is very ominous as the service faces this uncertainty.'
Briefings to RFA staff over the past month have confirmed that Treasury demands for a 10 per cent cut in the MoD budget have forced the possible shake-up.
Bob Crow, RMT general secretary, said: 'The government should be under no illusions. RMT will mobilise a political and public campaign on a massive scale to fight off any moves to privatise the Royal Fleet Auxiliary.
'There is no doubt there will be an angry backlash against any attempt to compromise national security by embarking on a cash-led sell-off of this essential lifeline to our naval crews all around the globe.'
A Royal Navy spokesman in Portsmouth said: 'The replenishment was purely an exercise and has no bearing on the review of the RFA, which aims to deliver value for money.'
>> Vote in our latest web poll.