The Conservatives said the figures demonstrate that the scheme has been a costly failure, but the Scottish Government said it was not designed to prosecute landlords but to provide reassurance for tenants.
Tory housing spokesman Alex Johnstone said: "This farcical programme, introduced with the best of intentions, is failing to deliver at a tremendous cost to the taxpayer.
"And responsible people with aspirations to get into the property business are being hit in the pocket because of this inadequate scheme.
"The private rented sector is playing an increasingly important role in delivering solutions to housing need in Scotland, and we need a robust an efficient mechanism to help achieve that.
"These figures suggest that, at the moment, the Private Landlord Registration Scheme is not it."