The PSRA has confirmed that only 40% of applications (2,000) received by the deadline of July have been accepted. The body has written asking the others to apply again.
Reasons given for the rejections include forms filled out incorrectly, missing data, details of qualifications that were not deemed relevant, cheques drawn out wrongly and incorrect tax clearance information.
It has also emerged that around 250 agents are being barred from providing professional property services because they sent their applications in late - and it could be well into next year before they get the opportunity to re-apply for a license.
Under new legal requirements, auctioneers, estate agents, lettings agents and management companies now need an operating licence issued by the PSRA.
A PSRA spokesman said: "This is a new process, and a number of unexpected issues have arisen - for example, the situation where accountants have told applicants that they can't get relevant tax clearance because they are jointly assessed.
"We've had to show them how to get such clearance from the Revenue Commissioners. It's quite a complex process for the applicants, and we've provided a 40-page booklet to tell applicants how to proceed."
