MINUSMA said troops "repelled a complex attack" on Saturday at their base in Ber, 60km east of Timbuktu, launched from several trucks armed with "rocket launchers, machine guns and other explosives".
A second attack in Konna, in the central Mopti region, involved a UN vehicle running over an improvised explosive device, wounding four Togolese peacekeepers, Al Jazeera reported.
"According to an initial toll, two peacekeepers were killed and several others were wounded," the UN mission said in a statement.
Burkina Faso army has confirmed that two of its peacekeepers were killed in the Ber attack, with five others were injured.
The UN has deployed about 12,000 troops and police in its MINUSMA peacekeeping mission in Mali, which ranks as the most dangerous country for blue helmets.
"I strongly condemn this brutal attack, which will not dent our determination to support Mali in its march towards peace," said MINUSMA chief Mahamat Saleh Annadif in the statement, adding that attacks against peacekeepers "could constitute war crimes".
Mali on Thursday extended by a year a state of emergency, in place since a deadly November 2015 attack on a hotel in capital Bamako claimed 20 lives.
The state of emergency was due to expire at the end of this month and the cabinet approved the extension.
It gives authorities greater powers to take measures to pre-empt attacks and accords more powers to security forces and judicial authorities, the government said.
Mali, the eighth largest country in Africa and one of the poorest in the world, has been struggling to return to stability after al-Qaeda-linked fighters took control of the northern areas of the country in early 2012, prompting France to intervene militarily.
The fighters were routed in a French-led military operation in 2013, but large stretches of the landlocked Sahel state remain out of government control.
Central Mali remains unstable owing to a resurgence of violence between ethnic groups, notably Fulani nomadic herders and Dogon farmers over access to land.
A peace deal between the government and armed groups was signed in 2015, but its implementation has been slow, while attacks continue in central and northern parts of the country.