More than 600 of the 800 employees at Porton Down are at risk of having their jobs relocated to Harlow in Essex.
The HPA proposed the move to a single site in 2010 but now the Department of Health wants at least another 12 months "to fully assess all the details".
Dorothy Fogg, from Unite, said despite uncertainty staff felt more positive.
The HPA has been responsible for responding to public health hazards such as swine flu since 2003.
In a letter sent to staff, the HPA said the government had requested a "considerable amount of additional work be done" on the business case for relocating staff to Essex which will "add a further year before the case is ready for resubmission".
Dr Christine McCarthy, the executive director of microbiology at the HPA at Porton Down, said employees had "anticipated a decision with a five year wait and now it looks like it will be six years".
"This is a very large investment of public funds - especially in the current climate - and they [the government] want as much information as possible to inform the final decision and they want to make the right decision,"  she said.
"But it's putting staff in a very difficult position - they have had two and a half years of uncertainty and this uncertainty is now going to be prolonged for yet another year."
But Dorothy Fogg, from the Unite union, said staff were also feeling optimistic about the decision.
"There's the uncertainty - they keep being told it will be sorted out year after year which causes frustration - but they're also feeling more positive," she said.
"And people are quite hopeful that when they review the case that they will hopefully recognise that it is better to keep the work and the people on site at Porton."
And MP John Glen said it was "very good encouraging news".
"What we're talking about here is spending possibly Â£300m on a very, very sensitive facility to deal with the most tragic circumstances in terms of public health so I think it's important that they get it right," he said.
"But what I think is interesting, in the letter that was sent to staff, is that Justin McCracken [chief executive of HPA] says that a decision in principle has not been made.
"I think that's an admission that the case has not been made and that those who work at Porton should be very reassured."
Hundreds of staff at the Health Protection Agency (HPA) in Wiltshire are facing another year of uncertainty over the future of their jobs.