Watch: At the scene of missile strike on Ukrainian theatre
Fifteen children were among 144 people wounded, the police said. At least 25 people were in hospital.
Among the victims were people who had been celebrating an Orthodox Christian holiday at church, the ministry said.
A main square and a university building were also damaged in the attack.
The UN called it "heinous".
Chernihiv is located around 50km (31 miles) from the border with Belarus. It was besieged by Russia at the beginning of the invasion.
The city's imposing theatre was hit directly. Tiles were blown off the roofs of neighbouring buildings with one catching fire 100 metres away.
The theatre was hosting a gathering of drone manufacturers, the acting mayor of Chernihiv told the BBC.
"I understand that their aim was a military event taking place in the building of the drama theatre and that it was their target," Oleksandr Lomako said.
"But it is clear that the Russians launching those missiles and those giving them orders in the middle of the day to the civilian city realised that the victims will be primarily civilians.
"There is no other way to interpret it than a war crime against civilians, yet another Russian war crime," he added.
The city centre of Chernihiv is a popular area for people to stroll around, especially on the weekend, locals told the BBC.
Anna Zahreba, the manager of a Crimean Tatar restaurant just across the street from the theatre, said her staff were getting ready for a busy day when the missile hit.
"I ran outside to see what was going on," she said. "There were two 12-year-old girls here and a lot of blood. One had her leg badly wounded. Another girl was screaming.
"We applied a tourniquet and waited for an ambulance. It was taking a long time to get here, but some man stopped his car and we took a girl to a hospital."
Anna says staff rushed to help injured people with medical kit and blankets.
"There are always many people walking around here, with children and baby strollers. Many restaurants and cafes in the area," she tells us.
"We did not expect a day like this."
Ukrainian President Volodymyr Zelensky said Russia had turned an "ordinary Saturday" into "a day of pain and loss".
Footage shows damage in Chernihiv's central square
The UN said it was "extremely disturbed" by the attack.
"It is heinous to attack the main square of a large city, in the morning, while people are out walking, some going to the church to celebrate a religious day for many Ukrainians," Denise Brown, the current head of the UN in Ukraine, said in a statement.
"Attacks directed against civilians or civilian objects are strictly prohibited under international humanitarian law," she said. "It must stop."
Three days of mourning have been announced in the city.
Moscow is yet to comment.
Elsewhere, Russia has claimed that a Ukrainian drone hit a military airfield in the northwest Novgorod region, causing a fire that was quickly put out.
One plane was damaged but no casualties have been reported, it added.
Ukraine has not commented on the alleged drone attack.
Meanwhile, Kyiv's air force said the Ukrainian military had shot down 15 out of 17 Iranian-made Shahed drones launched by Moscow in an overnight strike.