The number of people waiting more than 12 hours to be seen at accident and emergency departments increased by nearly 3,000, an Audit Office report reveals.
Delays have soared by almost 40% and are longest A&Es in Belfast, Northern and South Eastern Trusts, the figures show.
There are also long queues at outpatients, with almost 6,000 waiting five months or more for treatment, while it has been revealed 775 inpatients waited more than nine months.
It was noted that over the last two years the Health and Social Care sector did not reach the 95% target for patients waiting four hours or less for accident and emergency treatment.
The report looks at how the health and social care sector performed between March 2011 and 2012.
It also expressed concerns over the £2.8m bill footed by taxpayers because of false claims for eye and dental treatments.
Thousands of people in the region are cheating the system, and although more than 2,000 fixed penalties were issued during the year, only £30,000 was recouped from patients who failed to pay up.
The report said the Health and Social Care Sector's Counter Fraud and Probity Service (CFPS) should be given more resources.
"Northern Ireland Audit Office considers that CFPS's work should be supported by IT resources that facilitate the operational and strategic management of its activity and performance as well as the management of individual fraud investigations.
"This should enable a shift from reactive to more proactive/targeted activity, with a likely increase in both the efficiency and effectiveness of CFPS's work," the report stated.
During the year, random and targeted checks were carried out to identify the false claimants, while a further 104 referrals were made to the CFPS.
Of those, 39 came from the UK Border Agency, who found 39 people they suspected of being in NI illegally and accessing free health care. Nine cases were passed to the PSNI and two people were prosecuted.
In his fourth audit office report the Northern Ireland Comptroller and Auditor General Kieran Donnelly focused on the Health and Social Care sector which spends more than £4.4 billion a year.
Mr Donnelly said: "While 2011-12 was a year when the health and social care sector recorded good financial results it was also a period when a range of important measures of health care performance, including accident and emergency waiting times declined.
"The Department of Health, Social Services and Public Safety has noted some improvements in the early part of the current year. I will examine if this trend has been sustained in 2012-13."