The ESRI said there were 269,000 mortgages in negative equity at the end of last year.
According to the report, the number of home loans in negative equity peaked at 314,000 by the end of 2012.
The ESRI estimates that two in every five of these loans were in Dublin.
Since then, prices have risen sharply in the capital and have begun to rise in the rest of the country, albeit at a much slower pace.
The ESRI said three quarters of the 45,000 loans that are no longer in negative equity are in Dublin.
The report's author, ESRI senior research officer David Duffy, said negative equity can have harmful effects on the economy as it discourages those affected from spending and restricts their ability to move home.
Mr Duffy said the combination of property price increases and mortgage repayments since the peak of the negative equity problem in 2012 has reduced the extent of the problem, which he said is positive for the economy overall.