The Marshall Islands weather service says the capital Majuro could face several days of battering swells after the southern part of the atoll was inundated on Tuesday.
Large swells, combined with an unusually high tide brought on by this week's 'supermoon' have damaged many homes on the southern side of the atoll.
Locals says the waves passed straight over the atoll in some places and into the lagoon on the other side.
Reggie White, head meteorologist at the Majuro Weather Service, says waves reached around two-and-a-half metres.
"This morning was the highest tide for this particular moon phase," he said.
Mr White says this week's supermoon also played a part.
"Normally you wouldn't worry about a supermoon," he said.
"There's got to be an event that coincides with it and this was the high surf."
Mr White says the conditions could persist until Thursday and it is one of the more destructive tides he has seen on the atoll.
The weather service has issued a warning to residents on the southern side of the island to be ready to protect their homes.
Damage to homes
Majuro resident Provan Crump says the wave broke down one wall of his house in the early hours of Tuesday morning.
"I'm right on the ocean and it broke down my wall and we had water coming into the house at about five o'clock," he said.
"I reckon one wave put about a tonne of water inside the house when it broke down the wall."
Mr Crump says he's seen extensive damage and debris elsewhere on the island.
"There's a lot of rubbish washed half way through the island and in some places you could see the wave action had gone right across the island and into the lagoon," he said.
He says residents are all watching the swell in readiness for the next high tides.
"We'll be battening down the hatches and hoping for the best... that nothing else gets too badly damaged on the island." he said.
"The tides are a little bit lower, the swell might be a little bit smaller but it's still big enough that it will be coming up over the island again."
© ABC 2013
16:41 EDT Lightning strikes sparked fires in the roof spaces of two Canberra houses today as storms swept through the capital.