the UN's MINUSMA mission called the blockade a "siege" and said it had disrupted food supplies and forced healthcare workers and villagers to leave.
Boni - the capital of an area of some 29,000 inhabitants according to a 2009 census - is located near the RN16 national road which connects Mopti in central Mali to Gao in the north.
It has become one of the most dangerous roads in Mali.
The highway is strategic for the largely rural region that has been caught in a whirlwind of violence since 2015.
Jihadist groups in central Mali - a hotbed of violence in the Sahel - lay improvised explosive devices in the road ahead of army and MINUSMA convoys.
They also attack local civilians they suspect of collaborating with the military, punishing those who they believe do not adhere to their worldview.
"The Katiba Serma jihadists are blocking everything around me," a Malian from the Boni area now living in Bamako told AFP.
The Katiba Serma is affiliated with Al-Qaeda.
The Malian army, which has several bases along the RN16, has intensified its anti-jihadist operations in recent months with the help of what it says are Russian military trainers.
France and other former allies claim the Malian army is working with the private Russian private military company "Wagner Group" which has been accused of engaging in atrocities
Traffic on the RN16 remained blocked around Boni on Thursday.
"Buses and trucks are stuck in Douentza in the west and Gossi in the east," said a passenger in Douentza, speaking on condition of anonymity for his safety.
A worker from a bus company confirmed that "to go to Gao, it's blocked at Douentza -- our buses are no longer running.".
