The loch, near Inverness in the Scottish Highlands, can hold 7,452 million cubic metres.
But Sepa’s data showed the water level was at its lowest since the current loch level monitoring station began operating in 2016.
It is understood the unusual spell of dry weather in Scotland has been a reason for the level to go down.
A Sepa spokesman told BBC Scotland: "The western extent of the Ness catchment has seen drier than usual conditions in recent months, though the river levels Sepa monitor in the catchment have not been notably low.
"It's likely that the dry weather is a significant contributing factor to low water levels in Loch Ness."
The agency said lower levels had been recorded at the previous station in 1998, 1999, 2000 and 2010.