If confirmed, Monday's fighting will be the first time the Islamic Courts' fighters have clashed with forces from either of the country's two autonomous regions.
Since capturing Mogadishu, the Somali capital, in June, the Islamic Courts have pledged to extend their control over the whole of the East African country.
But the leaders of Puntland and Somaliland, two self-governing areas of northern Somalia, have said they will fight any attempt by the Islamic Courts to invade their areas.
On Monday, the Islamic Courts said that Puntland's forces had carried out a pre-emptive strike against their fighters who were gathering on the edge of Puntland.
"Puntland troops attacked us 30 minutes ago in Galinsoor area," an Islamic Courts source told Reuters on Monday morning.
Galinsoor is a town about 60km south of the approximate borders of Puntland.
"They attacked us with lots of heavy weapons and 'technicals'"
A field commander of the Islamic Courts
A commander in the field told Reuters that his men had been ambushed by a combination of Puntland forces and fighters loyal to a tribal leader whom the Islamic Courts ejected from Mogadishu earlier this year.
"They attacked us with lots of heavy weapons and 'technicals'," he added, referring to the Somali term for pickups turned into battle-wagons packed with guns and fighters.
There was no immediate information on casualties.
Authorities from Puntland could not be reached for comment.
The Islamic Courts captured Mogadishu and much of southern Somalia during the summer.
The movement's leaders say they intend to extend their rule over the whole of Somalia and over Somali-populated areas of neighbouring Ethiopia.
The Islamic Courts' aspirations directly conflict with those of the interim government which aims to restore central rule to the country for the first time in 15 years.
Sheikh Sharif Sheikh Ahmed, a main leader of the Islamic Courts
This government is closely linked to the Puntland's important clans.
Somalia's president, Abdullahi Yusuf, was the president of Puntland until 2001.
Thousands of troops from Ethiopia are said to be inside Puntland to bolster its forces and in the town of Baidoa where the interim government has its headquarters.
Addis Ababa says it has only sent a few hundred military trainers to Baidoa.
The northern half of Somalia is home to two self-governing states, Puntland and Somaliland.
Both regions have established functioning democracies and relative stability.
Somaliland, the better-organised of the two northern regions, has declared independence – although this has not been recognised by any other countries.