The Northern Ireland firm, which recently built the new ferry terminal extension at Sconser, Skye, secured the job with a £9.1m bid.
Works will take place on both sides of the river Ness between Friars Bridge and the mouth of the river near the harbour.
The scheme will raise the existing flood defences along both banks of the river in the form of low walls and embankments.
Another Irish firm Coffrey Group is working on the first phase of the flood £23m alleviation project between Ness Bridge and Friars Bridge.