All Eilat beaches were declared off limits to bathers late Friday night after hundreds of cubic meters of raw sewage began entering the Red Sea.
The Interior Ministry's action came after the city's sewage system ruptured in two places - near the port, and in the city's north. The cause of the leaks was unknown.
The breaches were repaired, but the sea water still poses a health risk, both for humans and for dolphins and other marine life. It is the third time in a year that sewage has flowed into the Gulf of Eilat.
The latest leak is expected to deal a significant blow to Eilat's tourism industry.
Yariv Abromovich, general-secretary of the Zalul marine environment group, expressed anger at the pollution. "It is [a degree of] neglect never seen before. Eilat Bay has the most sensitive ecological system in the country and it is unacceptable for one idiotic moment to destroy dozens of years of efforts."
Abromovich said Eilat Mayor Yitzhak Halevi had been "placed on the damning list of mayors who do not care for the upkeep of sewage systems."
If the Environmental Protection Ministry did not immediately open a criminal investigation, Zalul would file a police complaint, Abromovich said.