The incident took place at a refuse site in Enniskillen earlier this month leaving the victim, Ronnie Marshall, with serious injuries when his digger fell over and became partly submerged on 8 April.
He has now died in hospital.
Mr Marshall, who was in his 50s, was operating a digger at Drummee Waste Management Facility, which is at an old quarry.
It is believed the ground gave way and the digger fell into a gully and became partially submerged in water.
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Alex Baird, Chairman of Fermanagh District Council, which runs the landfill site at Drummee, said they were "devastated" by the death.
"We are devastated to learn of the death of Ronnie Marshall," said Councillor Baird.
"My thoughts and prayers are with the Marshall family at this very sad time.
"We are continuing to work very closely with the relevant authorities in their investigations into the cause of the tragic accident."
In a separate incident, a 60-year-old man has died in hospital from injuries he sustained while carrying out repair work at Dromoland Castle in Co Clare earlier this month.
Kevin Greene, from Lisdoonvarna, sustained burns to almost 30% of his body after he
became engulfed in flames while sealing a window at the hotel on April 4.
He died yesterday evening at St James's Hospital in Dublin.
The Health and Safety Authority and the Gardaí are both investigating the incident.
(BMC/VB)
