Around 30 homes and business were flooded over the festive period, with many rural roads closed due to high water levels.
Earlier at the Assembly, Agriculture minister Michelle O'Neill told MLAs the level of loughs Erne and Neagh had begun to fall.
The Executive meeting came hours after Secretary of State Theresa Villiers heard about the multi-agency response to the flooding on a visit to the Toome flood gates, which help drain Lough Neagh.
Northern Ireland has been allocated £1.3 million of the £51 million Chancellor George Osborne made available last month to aid the UK's flood response.
After the meeting at Stormont Castle, an Executive statement said: "The Executive today agreed to spend the full £1.3 million of additional funding for flooding on preventative measures and preparedness to mitigate future incidents."
The three departments dealing with the flooding - Environment, Regional Development and Agriculture - are to work with the Finance Department to bring detailed spending proposals to the next Executive meeting on January 21.
The statement added: "Ministers paid tribute to all those who worked through the holiday period in difficult and sometimes dangerous conditions to bring relief to those affected by flooding.
"There was a full discussion on how resources can be best used to limit the impact on people, properties and businesses.
"There was also an agreement the three ministers dealing with flooding would bring to the Executive proposals in relation to potential support schemes.
"The Executive agreed the approach must be balanced, supporting those in urgent need but also having a co-ordinated, strategic, evidence-based approach for the future."
Responding to an urgent Assembly question on the flood response, Ms O'Neill told MLAs: "Once weather conditions improve, an overall review of the response to the flooding experienced in the past two months will be carried out.
"The weather is forecast to become colder over the next few days, with less rain, and that will allow levels in the loughs to reduce further.
"They will, however, remain high, and Rivers Agency will continue to be on high alert."
On her visit to the Toome sluice gates, Ms Villiers pay tribute to all those who had helped in the relief effort.
"My heart goes out to those throughout Northern Ireland who have had their lives so severely disrupted," she said.
"It has been a devastating Christmas and New Year for many and it is vital for householders, farmers and businesses to get back on their feet as soon as possible.
"Over the past number of weeks, I have been moved by the resilience demonstrated by householders and businesses who have been working hard and with the help of neighbours to help each other deal with the impact of the heavy rain and flooding.
"Today I want to take this opportunity to thank all of those who have been involved in these efforts."
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