The warning came from the EPA yesterday as sign-ups continue to remain slow ahead of the deadline of February 1st next year.
There are around 500,000 septic tanks in Ireland but despite the €5 reduced fee offer ending last month, just 251,000 tanks have been registered to date.
The new registration scheme was introduced by Minister for the Environment Phil Hogan last February after the European Court of Justice ruled that Ireland was not doing enough to protect drinking water sources.
Since September 28th, the cost of registration has jumped to €50 but even when the charge was just €5 sign-ups were slow with many opposition groups describing the charge as an attack on rural Ireland.
The EPA insists all tanks will be inspected, however, with homeowners set to be given just 10 days notice of them taking place.
If there is a problem the property owner will be notified within 21 days of the inspection. Details of the works to be carried out will then be forwarded in another three weeks, with homeowners given a deadline to complete them.
The deadline will be based around the amount of work needed and owners who refuse to comply face the prospect of a fine of up to €5,000.