A flock of 6,000 turkeys has been diagnosed with the H5N8 strain of avian flu, the Department for Environment, Food and Rural Affairs (Defra) said.
Some of the birds at Low Farm in Fulstow, near Louth, East Lindsey, have died. The rest are due to be culled.
Defra said it was "unlikely to be directly linked to the previous case" at the nearby Austen Fen Farm.
A 1.8-mile (3km) protection zone and a six-mile (10km) surveillance area have been set up around Low Farm to reduce the risk of the disease spreading.
Chief Veterinary Officer Nigel Gibbens said: "We have taken swift action to limit the risk of the disease spreading with restrictions in place around the affected premises.
"A full investigation is under way to determine the source of the infection."
The protection zone at Austen Fen Farm, near Louth, was removed on 9 January but surveillance continued at the site, Defra said.
The same strain has been discovered in birds in Settle, North Yorkshire, a swannery in Dorset and flocks in Carmarthenshire, south west Wales.
Last month, the government introduced an avian influenza prevention zone, which lasts until 28 February, to help protect poultry and captive birds from avian flu after the strain was found in 14 European countries including Germany and France.
Bird flu has been confirmed at a farm in Lincolnshire four weeks after it was found at a nearby unit.