"And a large percentage of those taken in are not micro-chipped and therefore untraceable, with many of them young uncastrated males," says Dr Joe Collins, who was joined on the research team by Dr Vivienne Duggan and Sarah Finney of UCD and Professor Patrick Wall, chairman of Horse Sport Ireland.
Research has shown that much of the problem lies with the lack of breeding regulations.
There is no requirement here for the licensing of breeding donkeys - stallions or mares - or other controls on the keeping of non-neutered animals.
During the boom years of the early 2000s, there was a demand for novelty items of all kinds and it was generally considered that there was profit in the breeding of donkeys for sale.
Young donkeys, especially fillies, often traded for hundreds of euro each at fairs.
Fast forward a decade and while there is still a limited interest in donkeys - especially for showing - many are selling for nominal fees.
Others are being advertised 'free-to-a-good-home' through the various online market places, or, in far too many cases, being abandoned on waste land.
The cost of castrating the young males far outweighs their value.
In some cases donkeys have even been dumped on farmland, with farmers only discovering the additional animals days later.
Experts raised concerns donkeys may be seen as a low cost method of reaching the minimum stocking rate for ANC, particularly in the absence of requirements and inspections of specific equine welfare inputs such as buildings or shelters.
In order to claim such agricultural subsidies farmers have to demonstrate that the land is being farmed.
This generally means keeping, and demonstrating that they keep, qualifying livestock at a level above an agreed minimum stocking density, which are correctly identified and recorded.
The minimum stocking density, for example, has been fixed at 0.15 Livestock Units (LU) per hectare.
Cattle, sheep, deer, horses and donkeys qualify for use in the calculation of minimum stocking densities at varying LU value eg cattle over two years of age qualified as 1 LU each, the same as a donkeys.
However, subsistence farmers - by definition farming in disadvantaged areas of natural constraint - often find that the farming of cattle or sheep is a marginal or indeed loss-making enterprise. New rules regarding the keeping of horses introduced in 2012 also affected their numbers.
While applicants now have to show that their farm qualifies as an 'equine breeding enterprise' before the keeping of horses as qualifying livestock is permitted, donkeys continue to be eligible without the need to demonstrate any additional requirements.
They simply need to be appropriately registered with identification documentation showing the animals are in the ownership of the given applicant.
In 2011 there were 3,774 DAS applicants who registered 18,447 equines on the scheme. In 2012 there were only 1,469 applicants, who registered 6,768 equines.
The number of donkeys registered by persons not registering any horses for use on DAS/ANC in 2014 was 1,471 (in the care of 405 applicants) from a total of 5,156 equines (2,544 of them donkeys) in the care of 1,280 applicants.
The corresponding figures for the year 2013 were: 1,591 donkeys (from a total of 2,593 donkeys) in the care of 411 donkey-only applicants as a subset of 6,159 equines in the care of 1,436 equine-keeping applicants to DAS.
According to figures published for 2014, there were over 2,500 donkeys registered as Livestock Units (LUs) at a payment value of €1.6 million.
Galway and Mayo accounted for approximately one-third of that total number of both applicants and donkeys, with an average of 3.5 donkeys per applicant.
While DAFM has decided not to change the eligibility criteria for donkeys this year, it is believed that they looking at potentially restricting new donkey applications and/or the registration of new donkeys on existing applications.
There may also be a cap on the number of donkeys an applicant might register for use as Livestock Units (LUs), or otherwise capping the percentage of an applicant's LU requirement that he/she can fill using donkeys.
Animal welfare experts, however, are concerned that this may put an added burden on the animal welfare groups who are already struggling to cope with high numbers of abandoned animals.
These will include adult micro-chipped donkeys currently registered on Area Aid Schemes and as-of-yet unidentified juveniles (especially uncastrated males) with even lower monetary value than their current low market value.
"Each January we worry if new changes will be implemented and what affect it will have on donkey welfare," said Dr Joe Collins said.
"In light of this we now hope to meet with the relevant people to discuss the welfare, and the future of donkeys in Ireland."