He said the government knew the nationalities of five of the foreigners: Britain, Eritrea, Sweden, US and Yemen.
He said security forces identified them from their passports.
Mohamoud said: "We have successfully completed the operation against the terrorists who came here and we are chasing the other five."
He said the total number of fighters was 13, but earlier government officials reported they were as many as 35.
Earlier, Mohamed Abdulrahman Banga, Puntland's minister of information, said that the armed members of the Islamic Courts Union arrived in two fishing boats from southern Somalia, which they controlled for six months last year before being routed by Ethiopian troops sent to prop up a faltering interim government.
"They had their own small boats and guns. We do not know exactly where they came from - maybe from Ras Kamboni, where they were cornered in January," he said.
Fishermen said about a dozen fighters arrived on Wednesday, but Puntland officials said the number could be as high as 35.
Muse Gelle, the regional governor, said that area where the fighters arrived on Wednesday - the port of Bargaal - is a dense thicket, making it difficult for Puntland security forces to intervene on their own.
A radio station quoted Ade Muse, Puntland's leader, as saying that his forces had battled with the group for hours before the US ships arrived and used their cannons.
Muse said five of his soldiers were wounded, but that he had no information about casualties among the fighters.
Al Jazeera's Mohammed Adow said that members of the Islamic Courts Union were believed to be hiding out in the region since they were beaten in early January.
The target was reportedly a suspect in the 1998 bombings of US embassies in Kenya and Tanzania.
The destroyer's guns appeared to be targeting a single person, perhaps moving in a convoy, according to the CNN report.
The US launched air strikes in Somalia in January targeting three alleged al-Qaeda members but killing their allies instead, US officials have said.
Those suspects also were wanted for the embassy bombings, which killed 240 people.