Southern officials accused Sudan Army of raiding its base on Wednesday and injuring six people among them six soldiers.
"An SAF (Sudan Armed Forces) helicopter gunship attacked SPLA positions at Kiirabem, in North Bahr al-Ghazal, wounding four SPLA soldiers and two civilians," said Philip Aguer, spokesman for the ex-rebel Sudan People's Liberation Army.
He indicated the attack as part of efforts to disrupt the south’s independence referendum that will take place in January next year but a spokesman for the northern armed forces denied that any clashes had taken place.
SPLA Spokesman said the southern army was committed to the ceasefire and would not respond militarily.
Northern army spokesman al-Sawarmi Khaled said the claims were "absolutely not true". "We have not attacked anywhere near the border," he said.
The two armies stressed less than two weeks ago that they were committed not to return to war regardless of the outcome of the referendum, which may lead to independence for the south.
The head of the United Nations in Southern Sudan said that it could not confirm any attack but a UN team would be sent to the remote area to investigate.
If confirmed, this would be the second time this month that northern Sudanese force has bombed targets in south.
On November 13, northern aircraft bombed the south while fighting rebels from Sudan's Darfur region. Northern officials said the bombing was an accident.
Sudan's ruling National Congress Party has accused the south of supporting the main Darfur rebel group, the Justice and Equality Movement that fighting with Sudan Army.
"If you are accommodating these forces in the south, you are supplying these forces with weapons, logistics, petrol and cars," Mandour al-Mahdi, a senior official from the northern National Congress Party said.
"We think that this is a declaration of war against the north of the country," he told Reuters in this week.
He accused south Sudan administration for abhorring JEM rebels and giving centres to train it fighters.
South Sudan's army was not immediately available for comment on Mahdi's remarks, but it has already denies aiding rebels from Darfur.