A Status orange warning for winds is in place for Cork and Kerry from 10pm on Thursday. "Along with a spell of heavy rain and high tides there is a risk of coastal flooding and damage".
Issued this morning at 10:00am, the warning for these counties will be valid from tomorrow night at 10:00pm through to Friday morning at 9:00am.
The warning comes as Storm Callum is set to bear down on the country.
The Met Office has warned that homes and offices are likely to be flooded, with fast flowing or deep floodwater which could cause a danger to life.
It is due to pass to the west of Ireland, northern England and Scotland during Friday.
Storm Callum is expected to bring gale force winds of up to 150 kmph with torrential rain.
James Nicholas of Arriva Trains Wales said: "There is significant rain expected this weekend across Wales coupled with high winds and very high tides, particularly up on the Cambrian Coast - linking in to Shrewsbury". There is a chance of gusts of 70 to 80 miles per hour in the Western Isles during Friday afternoon and evening.
A road that was closed after an accident at Slieve Gullion forest park near Newry, Co Down, where a contractor working for Northern Ireland Water died after he was hit by a falling tree as Storm Ali wreaked havoc across Ireland.
"The strongest winds associated with this event will occur during the night-time hours and Friday morning rush-hour commute".
Wales and the North West could have the heaviest deluge.
A National Emergency Coordination group has now been set up in order to deal with the storm. The main impacts for the United Kingdom will be from heavy rain across some western areas on Friday and Saturday.
The county council is urging motorists to avoid all coastal roads, and to only make essential journeys.