Environmentalists have posted images on social media of trash covering several beaches, including plastic bottles and packaging with labels written in simplified Chinese characters - used in mainland China but not Hong Kong.
Speaking after a visit to a coastal area this morning, Leung Chun-ying said the refuse had been washed up in the city after heavy rain and floods struck southern China.
"A lot of domestic garbage was washed towards Hong Kong from the mainland... Predictably due to heavy rainfalls and floods in the past few weeks," he told reporters on Lantau Island.
"This is an extraordinary situation... We will follow this up with Guangdong relevant authorities," he said referring to the mainland province neighbouring the city.
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Flooding is common during the summer monsoon season in southern China, but rainfall has been particularly heavy this year and many areas have been lashed by torrential rains this week.
"If you actually look at the trash... It does not look like stuff you find in supermarkets here... This is not like our normally trashed beaches," Hong Kong-based green activist Gary Stokes, of Sea Shepherd Conservation Society, said on Facebook.
"Hong Kong creates more trash per capita than anywhere on earth, our track record on recycling efforts and cleanliness are dire," he said.
Domestic waste is deposited in landfill sites but also litters country parks, coastal areas and waterways.