The union welcomed the Commons science select committee findings that the Natural Environment Research Council has failed to make the case for merging the organisations on either science or cost grounds, or to consider the geopolitical role played by BAS in the South Atlantic.
Prospect Head of Research Sue Ferns said: "BAS is a world-leading research institute, and this report reminds us it is viewed as 'a jewel in the crown' of British science. If there is a case to be made on scientific grounds for changing its status we'd like to hear it – but as yet we haven't.
"Decisions of this importance must not be made purely on the basis of short-term financial considerations. Prospect does not oppose change for the sake of it but we have consistently argued that decisions on the future of public interest science must be based on an objective evaluation of impact and transparent consultation with stakeholders."
BAS research successes highlighted by the select committee include the discovery of the hole in the Antarctic ozone layer, the development of the Antarctic Treaty and the successful negotiation for a marine protected area in the Southern Ocean.
Ferns added: "The report makes clear that NERC's consultation on the merger has been confused and lacking in transparency, with a damaging effect on staff morale.
"It's about time the government started to recognise the value of the scientists it employs instead of inflicting ill-thought through schemes that have the potential to seriously damage Britain's capability and reputation."
Prospect represents 80 scientists, professionals and specialists at BAS, whose headquarters are in Cambridge, and 150 at NOC, based in Southampton and Liverpool. It has 80,000 members working for employers who carry out science, engineering or technology functions.