There are currently 2,079 children waiting for an autism spectrum assessment in Northern Ireland.
In the Belfast Trust area, children are waiting for up to 20 months to receive a diagnosis.
The shocking figures were revealed on Monday's BBC Nolan Show after pleas for help from despairing parents.
"There are many of you writing to me, asking for help," said presenter Stephen Nolan.
"You're saying you don't know what to do, that your child is desperate and that the authorities are not delivering.
"I looked at my emails over the weekend and there is a constant stream now of parents saying 'please do something for us'."
He revealed that the longest waiting time is in the Belfast Trust area, where children are facing a near two-year wait.
Of the 2,079 children currently waiting for an autism spectrum assessment in Northern Ireland, 279 have already been waiting for over a year.
They cannot get care packages or the specialised education they need without a statement of diagnosis.
Rodney Morton of the Health and Social Care Board told Nolan: "We are deeply sorry for the unacceptable delays - it's not what we want."
He said the system was modelled a few years ago on anticipating 1,500 children coming each year forward to autism services - but that number has increased to 3,000 children a year.
"We simply don't have the resources," said Mr Morton.
"We have been trying to secure additional funding.
"£2.8 million is what we're looking to address the gap in autism services. If we don't get that money I suppose regrettably I don't see any improvement in the waiting times at all.
"We've been asking for the money for the last 18 months."
Stephen Nolan responded: "Just let every elected representative hear that this morning.
"Let it ring around Stormont, let it ring around the new First Minister Arlene Foster and the Deputy First Minister Martin McGuinness who are at the top of the tree up there.
"They've been keeping children waiting for 18 months to give them funding and it's still not delivered."
Referring to the long-running row over Stormont's budget, he added: "Children have been caught up in politics for 18 months."
Waiting times vary across health trusts:
Belfast - up to 94 weeks
Northern - up to 65 weeks
Western - up to 50 weeks
Southeastern - up to 19 weeks
Southern - up to 12 weeks
Belfast Telegraph readers have responded to the figures with their own stories.
Co Antrim mum Emma Manton said: "The waiting times are a disgrace, my child was referred in July to the autism assessment team, this was 18 months after he was referred to paediatrics by our GP.
"We have had a phone call from the assessment team in our area to say they will send someone to do a school observation but it could be a year before he is fully assessed by the team. So we are two years into the journey looking at possibly another year.
"The lack of communication between teams and departments is shocking and there is such a reluctance to diagnose when research in other countries clearly states early diagnosis provides the best hopes and chances for these children."
Another mum Deborah Calvert said: "My son has been on the waiting list 20 months now since his first ASD assessment. I phoned the ASD service this morning and was told he'll be seen next month.
"It's an absolute disgrace, these kids need early intervention. Educational psychology is another service letting our children down, we shouldn't have to fight nail and tooth for these services, parents of kids with special needs are already stressed enough, we need help and support not more worry."
Carrickfergus man Ryan Hendry said: "This is getting beyond a joke now. I was diagnosed with Aspergers Syndrome (part of the ASD spectrum) back in 2007/2008. The process itself took almost two and a half years, and it's clearly not improving.
"The wider issue of mental health in this country has been allowed to fall to pieces, as the health service has been decimated."
Belfast woman Helena Hall-Booth said: "Absolute shambles. The folk on the hill have a lot to answer. Time to work for their money."