SEPA said the company claimed they had shipped wastepaper.
Officers investigated the bales of waste and found a range of household items, including used nappies, dog poo and aerosol cans.
The shipping came from the company’s materials recovery facility at Croy, about 20 kilometres from Glasgow.
SEPA chief executive Terry A’Hearn described the incident as “the most serious breach of the waste shipment regulations” in terms of the quality and quantity SEPA officers have witnessed.
Mr A’Hearn added these actions “risk undermining Scotland’s efforts to recycle, as stories like this create doubt in the public’s mind that the recycling they put out for collection will be appropriately managed”.
“I hope this prosecution serves as a warning to everyone that SEPA will not allow Scotland’s waste to become someone else’s environmental problem,” he said.
The recycling company usually sent wastepaper to its paper mill in Manchester, but a fire at the mill in June 2016 greatly reduced its capacity to receive and recycle paper.
As a result, paper was being exported for recycling abroad.
SEPA said officers “became aware of poor quality waste paper bales” on-site during a routine audit that year.
“The site manager was advised that all exports of waste paper from the site should immediately stop,” the agency said in a statement.
“SEPA requested paperwork for all waste that had been shipped and then made the necessary arrangements to stop any waste in transit so it could be returned for inspection…
“Between September 2016 and March 2017, SEPA officers examined a sample of bales from the 51 containers.
“A small number of bales were identified to be suitable for export, but the overwhelming majority were not.”