The minister said: "The precise impact on day-to-day activities will not be known until early Friday morning and the public - including schools and business owners - should keep informed of weather forecasts and make decisions based on local conditions".
Met Éireann has issued a status Orange warning for Clare and 12 other counties, with gusts of up to 130 kilometres an hour expected overnight tonight.
Winds of 50mph will batter Northern Ireland, southwest England and west Wales during Thursday night, spreading to Scotland by Friday morning.
A Status yellow wind warning is in place for counties Carlow, Kildare, Kilkenny, Laois, Longford, Offaly, Westmeath, Cavan, Monaghan, Leitrim, Roscommon, Limerick and Tipperary, from midnight on Thursday until Friday morning.
Met Éireann forecaster Deirdre Lowe said strong winds would be followed by a period of heavy rain sweeping up from the south east, with the possibility of flooding.
Arriva Trains Wales is warning passengers to check before they travel as services may be disrupted.
"Some exposed locations could see as much as four inches by the end of Friday".
While heavy rain is expected to continue into Saturday, the wind is now forecast to ease off by Friday evening. Even though the high winds will be the main concern, a spell of heavy and possibly thundery rain will occur too, making for an extremely windy and wet start, with squally conditions associated with the secondary cold front as it tracks north-eastwards up across the country.
"Despite clearance efforts by the Council, the high winds will increase the amount of falling leaves and block drains very quickly, exacerbating flooding" he warned.
"The rain is expected to be accompanied by strong winds, which when combined with high tides may lead to some coastal impacts due to large waves".
Shropshire is on the edge of the yellow warnings we have issued, with the most persistent and heaviest rain expected across Wales, north west England and south west England.
On Tuesday, heavy rain caused widespread floods and landslides in parts of Scotland.