US marines have denied that they landed on Somaliland's coast and questioned locals about terror suspects.
A US anti-terror base is as close as it could be to Somalia
Fishermen and officials said that two boats carrying 20 marines had landed and handed out photographs before sailing back into the Red Sea.
But the commander of the US anti-terror base in neighbouring Djibouti said no marines had gone ashore in Somalia.
Gen Samuel Helland suggested the reports may have been confused with a training exercise in Djibouti in April.
Somaliland's declaration of independence from the rest of Somalia has not been internationally recognised but it has enjoyed relative peace.
"It's a fabrication of the exercise off the coast of Djibouti," Gen Helland said.
"To my knowledge there has been no Marine activity off the coast of Somalia other than the 5th Fleet ships sailing by on their way to Iraq," he said.
Somaliland officials say they have complained about US helicopters entering its territory without permission.
Locals said the marines had spent about three hours in the village of Maydh on Tuesday but it was not clear who the marines were reportedly looking for.
"They met some of the fishermen and the people and they showed some pictures they were carrying, saying that these people are terrorists that they are trying to capture," said Assistant District Commissioner Ali Abdi.
Three US ships, including a helicopter carrier were also spotted in the port of Las Qorei.
The BBC's Hussein Ali Nur in the capital, Hargeisa, says there is no history of terror groups working in Somaliland.
The authorities accuse terror cells based in Mogadishu of carrying out four killings of expatriates in Somaliland in 2003 and 2004.
Western diplomats say that terror cells operate in the anarchy of the rest of Somalia.
Somaliland has an agreement to work with the US forces in Djibouti.