Floods: Lough Neagh water levels at 30-year high
David Porter of the Rivers Agency said levels at Lough Erne were also rising again after an initial fall off.
He said they were pumping water out of properties near Coalisland in County Tyrone.
Armagh Observatory said December had been the wettest on record at the institute.
It said the total amount of water recorded as falling was nearly 7.33 inches (18.61cm).
However, it said it was also the warmest December at Armagh since 1988.
Agriculture Minister Michelle O'Neill visited homes affected by flood water outside Lisnaskea, County Fermanagh, on Tuesday.
Ms O'Neill said it was "very evident" that for some residents the only suitable form of transport on some roads was a tractor.
She said the flooding was causing difficulties to everyday life and "massive challenges for those who live around Lough Erne, particularly in Fermanagh".
"What I wanted to do was to go out and reassure those people in rural Fermanagh that Rivers Agency are doing everything that they can," she said.
"I think that was very evident on the ground and people did accept that. "They accept that they live near Lough Erne and there's always going to be problems with the lough."
A number of roads in the county still remain closed.
Among the properties Ms O'Neill visited was the home of Gary McManus, who has taken a week off work to care for his mother who is in her 80s, because her care assistants cannot access the property.
Derrytresk on the shores of Lough Neagh near Coalisland is also affected.
Jimmy Quinn said water has been pumped away from his house and his neighbour's since Boxing Day.
"You know you're in a bad way when you see the swans swimming past your window when you are watching Coronation Street," he added.
Ms O'Neill said a task force was set up in 2009 following severe flooding in the area near Lisnaskea.
"A lot of work was done in terms of raising roads," she added.
"Unfortunately I think that needs to be reviewed again, because some of those roads that were actually in fact risen, maybe by as much a metre at that time, are actually under water again."