There have been 168 confirmed reports of toxic blue-green algae in waterways across Northern Ireland since May.
With public concern growing over the impact of the algae at Lough Neagh, the chief executive of the Northern Ireland Environment Agency (NIEA) has warned there is no quick fix to the problem.
Paul Donnelly also said that a working group is being put together to examine how to combat the algae, but said it would be easier to make spending decisions with ministers in place at Stormont.
Officials from the Food Standards Agency (FSA) and Northern Ireland Water (NIW) have insisted there is no risk in eating fish caught commercially in the lough or to drinking treated water.
Lough Neagh is the biggest freshwater lake in the UK or Ireland.
It supplies 40% of Northern Ireland’s drinking water and sustains a major eel fishing industry.
Noxious blooms of algae have covered large parts of the lough across the summer.
Other waterways and beaches in Northern Ireland have also been impacted by the issue.
During a media briefing, Stormont officials said algae growth is linked to excess nutrients in the water.
Nitrogen and phosphorus from agricultural fertiliser running off fields is believed to be a major contributory factor.
The spread of the invasive zebra mussel species is also understood to have played a role, as they have made the water clearer, allowing more sunlight to penetrate, stimulating more algal photosynthesis.
Climate change is another factor cited, with the highest ever water temperature at Lough Neagh recorded in June.
The deaths of birds and dogs have been linked to the recent algae blooms.
A number of water-based businesses on Lough Neagh have also had to stop operating.
Gareth Greer, from the water management unit at the NIEA, said: “As of September 14, we have 168 confirmed reports of blue-green algae, these are across 65 different locations.”
The majority of the reports have been around Lough Neagh but they have also spread along the River Bann and reached beaches on the north coast.
Mr Donnelly, of the NIEA, which is part of the Department of Agriculture, said a working group is being put together to examine issues such as water quality.
He added: “We are going to task that group to do a review of policies, a review of the regulations, a review of the knowledge, transition and behavioural change.
“That is important work, we have set ourselves the target of around 10 weeks to do that to try to develop a plan to map out a way forward so we can make an impact here.
“There is no quick fix to this problem. It has been a long time in the making and it will take a bit of time to solve.”
He added: “If we had ministers (at Stormont) that would help the situation because this is not going to happen quickly.
“It is going to cost money, we do need investment, investment in people, resources to bring forward some of the actions that are going to be needed.
“It would be more helpful to have ministers in place to help us push this forward and take decisions that are going to need to be taken.”
Robin May, chief scientific adviser at the FSA, said there were no concerns about eating fish harvested from Lough Neagh by commercial fisheries.
He did advise that people should exercise caution about eating fish caught by private anglers from the lough.
Dymphna Gallagher, head of drinking water regulation at NIW, said: “We can give complete assurance that drinking water from Lough Neagh, taken to our treatment works and treated, is safe to drink.
“There is a great distinction between direct contact with blue-green algae in raw water and what you get in your tap.”