It is believed the hallucinogenic drug is being put into boiled sweets to avoid arousing suspicion from door staff at bars and nightclubs.
Dealers are trying to sell the drug to students in particular, the NCA said.
The warning follows an ongoing criminal investigation in which almost half a litre of LSD was seized in Manchester.
The NCA said the confiscated liquid would be enough to make more than 5,000 sweets.
LSD is usually sold after being infused into small squares of blotting paper.
A statement from the NCA said: "We are asking that staff at entertainment venues be vigilant and consider refusing entry to customers or groups of customers carrying small amounts of such sweets.
"Students should also be wary of anyone offering them drugs in this form.
"Any such incident should be reported to police immediately."
Drug dealers may be selling sweets laced with LSD across Greater Manchester, the National Crime Agency has warned.