Human health and the environment are still being put at risk by an illegal landfill site that started operating at least 17 years ago.
The Kouroupitos site on the Greek island of Crete, which has been taking waste since 1988, was first clamped down on by the EU five years ago.
Greece was fined €20,000 (£13,700) every day for almost eight months until the European Commission accepted it had shut the site in 2001.
A spokesman for the EU said: "The new case focuses on the failure to clean up the Kouroupitos and Messomouri sites.
"A report produced for the Commission by independent experts in 2003 pointed to several problems at both sites that posed risks to human health and the environment.
"At the Kouroupitos dump, soil had been put over the site to cover it but much had been washed away by rain.
"Waste was still burning inside the dump, causing potentially toxic emissions. Concern was expressed about the stability of the site and a potential risk of landslides as a result.
"The Messomouri site had become an illegal dump. Many of the bales of waste stored there had burst, and high concentrations of methane gas were measured.
"Liquid from the site was not being collected or treated but was flowing into a ravine that leads to the sea."
The final warning comes after Greece replied to an earlier letter by saying that clean-up plans had been drawn up for both sites, but no funding had been secured to carry them out.
If Greece fails to heed this latest warning, the Commission can take it to the European Court of Justice, where the country faces a fine.