People preparing for gender reassignment are being treated as second-class citizens by the NHS in England, with many taking at least six years to go through the process, according to the state-funded watchdog Healthwatch.

Katherine Rake, its chief executive, said those seeking to change their gender often faced an “incredibly troubling” experience, with the process taking “a considerable part of people’s lives”.

A support group for transgender people also warned delays were leading to patients considering self-harm and suicide.

Campaigners said it was vital the NHS honoured 18-week targets that should cover both referrals of patients by GPs to one of the country’s seven specialist gender identity clinics, and, later, their listing for surgery.

At present, many people wait for over a year even for an appointment at a clinic. Others, after years of treatment in preparation for surgery, face an average wait of nearly two years for operations at the busiest centre for people transitioning from male to female.

In between, there are problems in getting funding from local health commissioners and arranging voice therapy and hair removal.

Patients would be lucky to complete their transition in six years, said Rake. “Clearly, this is a very major procedure and the uncertainty is being combined with delay. One can only imagine the sense of anticipation prior and through the process. The longer it goes on, the more frustrating it must be.”

Healthwatch warned matters would only get worse unless there were big improvements.

UK Trans Info, the volunteer organisation that seeks to represent the interests of transgender people, said services were in crisis. The NHS had regarded them as low priority and only recently accepted patients had a legal right to access services within 18 weeks.

Jessica Coal, a spokeswoman at UK Trans Info, said: “We regularly speak to people who are actively self-harming or considering suicide due to delays and lengths of waiting lists for gender clinics or surgery.

“Importantly, many of them will not seek help because they believe it may put their treatment at risk if they show any signs of instability,” Coal said. “The delays and other problems with gender identity services are putting lives at risk.”

Joanne Clements, 58, from Hampshire, who underwent treatment in London over six years and works with a local charity helping others, said that although staff were professional, administration of services seemed totally overwhelmed.

“Treatment delays can lead to a lot of self-medicating, which causes problems in itself,” she said.

Some people looked at private treatment: “Some of that is cheaper if you go abroad, but some of those services can be very dodgy and lead to more problems which the NHS will then have to deal with.”

NHS England said about 3,000 patients each year were at some stage on their care pathways, two-thirds of them trans women – seeking male to female reassignment surgery – at an annual cost to the NHS of more than £17m. About 330 surgical procedures were carried out in 2014-15 by a handful of specialists at four centres, in London and Brighton for trans women, and in London for trans men. NHS England says it is meeting its 18-week surgery target for transmen.

Will Huxter, chairman of NHS England’s gender identity services task and finish group, said: “The NHS put additional funding into gender reassignment services last year and will continue to do so.”

Imperial College healthcare NHS trust, which runs Charing Cross hospital in London, where the average wait for gender reassignment surgery is now 102 weeks, said it agreed with NHS England “that our gender reassignment patients should receive the same services and rights as all other NHS patients and that they should be seen and treated as quickly as possible”.

A spokesperson said: “We are working with NHS England and the private sector to agree a plan to recruit more surgeons, increase capacity and reduce the waiting time. Our objective will be to reduce the waiting time for surgery to less than 18 weeks, in line with the national target for treatment to begin within 18 weeks of referral.

“We are working to agree with NHS England the detail of exactly how this target should apply and be reported for this patient group.”