The male crocodile 'Lolong', was captured in the Agusan marsh on the southern island of Mindanao last September.
It followed a two-year search after a girl was killed and a fisherman went missing.
Guiness says the crocodile was weighed at a nearby truck weigh-bridge and was found to be more 1,075 kilograms.
Welinda Asis Elorde, media affairs coordinator for the town of Bunawan, which has custody of the new record-holder, says the local government had received an official certification from Guinness.
"He's doing well. I think he has already adapted to his new environment," she told the AFP news agency.
Ms Elorde says 'Lolong' was originally fed the equivalent of 10 per cent of his body weight in beef, pork and poultry every month, but an expert put him on a diet to get him to be more active.
"I was there (at the crocodile park where Lolong is kept) yesterday and he remains a big tourist attraction," she said.
"Hundreds of people visit him in a day."
The Guinness record was previously held by Cassius, a 5.48-metre Australian saltwater crocodile weighing close to a tonne.
Cassius has been kept at a crocodile park at an island off Queensland since his capture in the Northern Territory in 1984.