The Momentum Skills Pathways and Fresh Start programmes - which help people who have suffered from strokes, brain haemorrhages or suffered head injuries in attacks and accidents - are to shut at the end of June after council bosses withdrew their funding.
Six employees will be made redundant and around 25 service users will be left without the lifeline, the only programmes of their kind in Glasgow.
The support groups also help people with mental health problems, including anxiety and stress, by building confidence, improving physical stamina and helping them to find work placements.
Staff were left devastated when they were told that the services were to shut and they would be out of work from June 30.
Dozens of service users have been left angry and upset by the decision and some say the news has brought back feelings of stress and anxiety which they were receiving help to deal with.
David Reid, 26, of Sandyhills, started on the Pathways programme in August last year after suffering from encephalitis, a serious medical condition causing brain inflammation.
David said: "I'm angry not just for me, but for the future service users too who will need help.
"It is a feeling of hurt.
"The emotions that we're trying to work on at the sessions, like anger, worry and stress, that's all the feelings which are coming back now.
"It is opening up a can of worms as we felt we had support and that we were covered.
Other service users are not only worried about what they will do for support in the future, they are baffled by the council's decision to withdraw funding and are demanding answers.
James Gow, 40, from Maryhill, said: "The Southern General has the most advanced neurological department in Europe, so why is the city cutting the aftercare services which are needed to go along with it?
"It just doesn't make any sense."
The non-profit organisations, which had been running for more than a decade, have helped hundreds of people return to normal life after suffering often traumatic head and brain injuries.
A letter issued internally to staff said: "Our main priority at this time is to ensure the best possible outcome for the people we support and we know that this will be a difficult time for them as they come to terms with the news.
"This decision by Glasgow City Council has created a huge sense of loss in Momentum as we lose services which have made a direct difference to the day-to-day lives of many people in Glasgow who have suffered an acquired brain injury or had mental health difficulties."
Philip Bell, the centre's freelance art tutor, has been working with different clients for more than 12 years.
He said: " It is absolutely disgraceful.
"All of these people are trying to be contributing members of society, and the council are just stopping them from doing that.
"It's the one thing that they're crying out for them to do - come off sickness benefit, get back to work.
"These people are trying to change their lives but the rug has been pulled out from under them."
Another member of staff, who did not want to be named, said: "A lot of things have been taken out of our hands - this is a management decision and there's nothing we can do.
"Morale is really low amongst staff and we just have to go on the best we can with the clients.
"I feel sorry for them; the work we have done to get them to this stage is fantastic, but to take things away at this point is no good.
"Rehabilitation is totally different and we're the only place in Glasgow that does it."
A council spokesman said the reason for the funding cuts was due to the service "failing to help people into employment".
"Social work can not justify continued investment of significant funds into organisations which fail to produce required results for people," said a spokesman..
"The majority of the people were referred to the programmes from health services which can offer alternative employability services."