The operation on Friday in the port city of Guayaquil, in south-eastern Ecuador, also netted three arrests, including one foreigner, who were ordered jailed, said the prosecutor's office in a post to their Twitter page.
The liquid, which authorities said was liquid cocaine hydrochloride, was declared to authorities as a shipment of disinfectant, prompting the suspicion of police.
"A company making its first export declared 7,000 liters of disinfectant, which it said was bound for Valencia, Spain," said Interior Minister Jose Serrano.
"This amount called the attention of police personnel, who opened the container to verify the product," and found the drugs, he said.
So far this year, authorities have seized 38 tons of drugs, mostly cocaine, Ecuador said.
Drug cartels, including Mexico's Sinaloa and others from Colombia, hire bands to transport the drugs from the border to the coast for shipment.