PHE submitted an outline business case for the creation of an "Integrated Science Hub" to the Treasury in July 2014. Moving around 600 jobs to the former GlaxoSmithKline site in Harlow was cited as the "preferred option" on economic and science grounds.
Clive Scoggins, the Prospect negotiator responsible for PHE, said: "The news that this move has been agreed by the Treasury is disappointing.
"Prospect and our sister trade unions in PHE have been expressing deep concern over the impact of these proposals on employees for many years.
"We are aware that most of our members and their families are established in the area and a move to Harlow may be untenable.
"It is also difficult to see how PHE will be able to replace the extremely specialist scientific skills developed by staff working at Porton, should they be unable to relocate."
He said assurances had been given that the earliest the functions would transfer is in 2019.
"In the interim Prospect will, alongside our sister unions, work closely with PHE to ensure that policies are put in place to assist employees to relocate without suffering detriment or if they are unable to move, that they are treated fairly and supported in finding alternative employment."
The current funding only covers the relocation of laboratories from Porton Down to Harlow.
Funding for associated moves from PHE sites at Colindale and Whitechapel remains subject to a spending review later in 2015.
The vaccine production section of the business at Porton was spun out to a new company, Porton Biopharma, earlier this year and will not be relocating.