Prospect national secretary Tony Bell said: "This decision represents a victory for common-sense, a victory for science and a victory for staff.
"It will help to end the uncertainty that faced dedicated scientists and professionals in both institutions, enabling them to get on with their jobs and continue the ground-breaking research that has built the iconic status of these institutions.
"We are still awaiting the details behind the decision and it is not yet clear how NERC intends to proceed with plans to reduce capital expenditure on research ships and other large infrastructure items covering both marine and polar research. There are also still concerns about the separate decision to seek 18 volunteers for redundancy in science areas at BAS, as well as cuts in facilities and support.
"However, the decision not to proceed with merger vindicates Prospect's long-held view that the future of public interest science should not be sacrificed for short-term cost savings. We are glad NERC has listened to the people who deliver."
Prospect represents 80 scientists, professionals and specialists at BAS, whose headquarters are in Cambridge, and 150 at NOC, based in Southampton and Liverpool.