The free use of groundwater must stop before the end of the year or Malta may face legal action, according to the European Commission.
The government, however, yesterday insisted no charges would be introduced this year.
The introduction of water pricing policies by 2010 is mandatory in all EU member states according to Article 9 of the Water Framework Directive. The price tag attached to groundwater should provide adequate incentives for its efficient use - which means it must be metered and charged.
Last week, the government published a legal notice making the installation of meters at boreholes obligatory. But a ministry spokesman told The Sunday Times yesterday that no charges would be introduced this year in relation to extracted water.
However, a spokesman for the EU's Environment DG said: "The provisions on water pricing are required to be implemented by the end of 2010 at the latest."
He told The Sunday Times that plans for the protection of groundwater should have been submitted to the Commission by March, and by that time they should have been subject to compulsory public consultation for at least six months.
"According to the information available to the Commission, Malta has not yet published the draft plans for public consultation due in December 2008, meaning that it accumulates an important delay in the implementation of the directive. The Commission may consider taking legal action for this delay," the spokesman said.
The Resources Ministry said the metering process initiated last week will be implemented for the 8,000 registered boreholes.
Priority will be given to commercial boreholes, particularly those from which a substantial amount of water is extracted. The boreholes used for agriculture will also be metered, but the cost of the installation will be subsidised "to protect the farmer from lack of water".
"At this point, we will only be monitoring. We need a more profound analysis of what is being extracted. If we introduce payment immediately, we will not get a real picture," a ministry spokesman said.
He added that over the past months the government took "drastic measures" for the water resource to be sustainable. Two legal notices were published in 2008 requiring the notification of boreholes and a moratorium on the drilling of new boreholes is still in place.
The government also launched a registration scheme for water tankers drawing from the water table. The Malta Resources Authority (MRA) received 86 applications from operators of water tankers for a total of 126 vehicles.
A recent environment report drawn up by the Malta Environment and Planning Authority concluded groundwater extraction is a serious cause for concern. The report shows that over-extraction is leading to salt water seeping into the water table, increasing salinity levels.
Moreover, some of the perched aquifers have been completely decommissioned from the public supply because nitrates exceed the EU limit by more than three times.
According to the MRA, the free use of groundwater for commercial, private and agricultural purposes has led to the annual extraction of around 11 million cubic metres more than the sustainable capacity of Malta's aquifers.
In spite of warnings from the Commission, and admissions by the Resources Ministry that Malta will fail to meet this year's deadline, the MRA said: "Malta is, and will be compliant with the Water Framework Directive".