"More than 45 civilians were killed when the Islamic State took over (on Tuesday) -- they burned down houses, the market and other places," the Malian official said.
"What really worries us is the humanitarian situation -- the people are on their own."
The attack occurred at Talataye, about 150 kilometres (90 miles) from the city of Gao.
The raid was followed by intense fighting between them and other armed groups in the region, including rival jihadists who have pledged allegiance to Al-Qaeda, the sources said.
An agglomeration of hamlets, it has been battered by fighting in Mali's decade-long security crisis, lying at the heart of competing areas of influence.
An official from the Movement for the Salvation of Azawad (MSA), one of the armed groups involved in the clashes, put the civilian death toll at 30 and said many people had been displaced.
"The fighting between the various jihadist groups resulted in the deaths of several dozen civilians", said an international humanitarian worker in the region, also speaking on condition of anonymity.
"Some wounded who could not be helped died afterwards".
One of the poorest countries in the world, landlocked Mali has been battling separatist and jihadist insurgencies since 2012.
Jihadist-fueled violence began in the north and then spread to the center of the country before reaching into neighboing Niger and Burkina Faso.
Across the three countries, thousands of civilians, police and soldiers have died and millions have fled their homes.