The 34-year-old has not been seen since he started a trek to a waterfall in Tioman Island, off the south-eastern coast of the country's mainland, last Tuesday morning.
The body, which has not been confirmed as the missing Briton, was found yesterday in a pond a few yards from a kayak storage unit near the Juara Turtle Project where Mr Huntley had been working, according to local reports.
A Foreign Office spokesman said: "Malaysian police have confirmed that a body has been found on Tioman island in Malaysia.
"Foreign Office consular staff on the ground are continuing to work closely with the Malaysian authorities and are investigating with them as a matter of urgency.
"We continue to provide support to the family of Gareth Huntley at this very difficult time."
A search party consisting of commandos, police and firefighters stumbled across the body when they were returning to the base camp at around noon local time, Malaysian newspaper The Star reported.
It was behind a row of cabins which were occupied by rescue teams over the last three days, the paper reported.
Mr Huntley, of Hackney in east London, who is originally from the Leeds-Bradford border, was on a sabbatical from his job in the City when he went missing.
His mother, Janet Southwell, arrived in Malaysia on Monday after Prime Minister David Cameron spoke to Malaysia's Prime Minister, Najib Razak, about the search effort.