For the past 10 days, civil society groups have shared images of trucks carrying rubbish and tipping it into the Mediterranean, a process that is ongoing.
Activists say the waste from the "mountain of garbage" at Borj Hammoud in north Beirut is disposed of under an agreement between the government's Development and Reconstruction Council (CDR) and a private company.
"They are taking garbage from this mountain that has been there for 20 years... and throwing it into the sea," said Wadih al-Asmar, an activist from the "You Stink" campaign behind the protests in 2015.
Environment Minister Tarek al-Khatib on Tuesday confirmed the existence of an agreement between the CDR and a private firm to dump the waste at sea.
Khatib said he had sent letters to the CDR to "rectify" the situation and that he was trying to find the "best way to limit" the damage.
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But activists vented their anger on social media, branding the situation "shameful".
"Waste is thrown into the open sea and the environment minister justifies it... he gives them the green light," said the You Stink campaign.
Asmar, the campaign activist, denounced the disposal of the garbage at sea without any treatment, saying it was "killing the marine ecosystem".
Lebanon experienced a major waste crisis in mid-2015, with garbage piling up in the streets of Beirut and its surroundings after the closure of the country's main landfill.
This crisis triggered mass protests, with many taking aim at politicians in a country that has suffered endemic corruption since the end of the 1975-1990 civil war.
In 2016, the government decided to reopen the landfill and to create two more dumps, one in Borj Hammoud next to the "mountain of garbage" whose stench fills the air in the capital's northern suburbs.