"As I speak a lot of shots are being fired in Kidal. Armed men are shooting and the Malian soldiers have retaliated," Adama Kamissoko told AFP by telephone from the city.
"I do not know exactly who is firing against the Malian army, but it is defending itself."
A source from the governor's office said the gunmen were Tuareg separatist rebels from the National Movement for the Liberation of Azawad (MNLA), which pulled out of peace negotiations with the government on Thursday.
He added that international troops and peacekeeping forces present in the city were not yet involved in the fighting.