Although the Department of Health insists that the trust's work on this issue remains a priority, the move will leave it battling to fill the funding gap caused by the loss of income.
HIV and Aids charities have struggled to ignite widespread public support for their cause and increasingly rely on statutory funding to pay for campaigning work in this area.
The decision will lead to the trust's first redundancy. The senior role of campaigns manager, held by Keith Winestein, will cease to exist after the funding ends on 30 September.
Winestein has been a pivotal force in the charity's work over the past five years and in 2002 launched the national 'AreYOU HIV- prejudiced' campaign, which has been the backbone of NAT's campaigning work.
Trust spokeswoman Emma Bickerstaff said: "Getting funding for HIV policy and campaigning is not easy. We will need to find alternative sources if we are to continue the work."
Launched in 2002 as part of the Government's sexual health strategy, the trust's "AreYOU HIV-prejudiced" campaign has included posters, bus sides, cinema ads and a website to challenge perceptions about people with HIV and Aids.
The Department of Health said the move signalled a shift in the direction of its work on HIV/Aids.
Although decisions are yet to be finalised, the DoH said funding will be redistributed across the voluntary sector in contracts designed to concentrate on more targeted interventions.
Bickerstaff said the trust would apply to the DoH, corporates and other bodies for funding for targeted one-off projects such as tackling stigma in the workplace.