Danish police said it was too early to link the latest attack, which took place in the Krystalgade area of the city, to the earlier shooting.
The condition of the victims was unknown and the gunman fled from the scene on foot, a police spokesman added.
Police, who said the first shooting was likely to be a terrorist attack, were still hunting the gunmen last night.
They confirmed a 40-year-old man had died after attending the Art, Blasphemy and Freedom of Expression café event, where the French ambassador to Denmark was one of the speakers.
Witnesses claimed “at least 50 shots” were fired during the organised event, which was also attended by Swedish cartoonist and historian Lars Vilks, who once drew the Prophet Muhammad as a dog.
Vilks and French ambassador François Zimeray were not harmed in the attack.
Bullets ripped through the window of the Krudttoenden café, known for its jazz concerts, just after 3:30pm.
The meeting had been held under tight security, with delegates subject to searches as they entered the building.
Satire researcher Dennis Meyhoff Brink, who was also present at the debate, said that he heard 30 shots over a two-minute period.
The attack comes just over a month after gunmen stormed the Charlie Hebdo offices in Paris, killing 12 people.
Niels Ivar Larsen, one of the speakers at the event, said: “I heard someone firing with an automatic weapon and someone shouting. Police returned the fire and I hid behind the bar. I felt surreal, like in a movie.”
Helle Merete Brix, one of the event’s organisers, said that Vilks was at the meeting but not injured.
“I saw a masked man running past,” she said.
“A couple of police officers were injured. I clearly consider this as an attack on Lars Vilks,” she added, saying she was ushered away with Vilks by one of the Danish police guards that protect him whenever he is in Denmark.
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Zimeray, the French ambassador to Denmark, tweeted that he was “still alive” following the shooting, where he was one of the speakers.
He later said: “They fired on us from the outside. It was the same intention as Charlie Hebdo except they didn’t manage to get in.
“Intuitively I would say there were at least 50 gunshots, and the police here are saying 200.
“Bullets went through the doors and everyone threw themselves to the floor. We managed to flee the room, and now we’re staying inside because it’s still dangerous.
“The attackers haven’t been caught and they could very well still be in the neighbourhood.”
About 30 bullet holes were seen in the windows of the Krudttoenden café in the north of the city after the attack yesterday and at least two people were taken away on stretchers, local channel TV2 said.
The local Berlingske newspaper said one spectator was seriously wounded and three police officers were lightly wounded.
Danish Police, who tonight were still hunting the gunmen, erected cordons around the café and searched a nearby park.
They said that the suspects spoke Danish.
In a statement, Danish police said the victim was a 40-year-old man inside the café attending the event who had not yet been identified.
Police spokesman Henrik Blandebjerg said three police colleagues at the event were also shot.
French foreign minister Laurent Fabius condemned the attack, saying in a statement that France “remains by the side of the Danish authorities and people in the fight against terrorism.”
Vilks, a 68-year-old Swedish artist, has faced several attempted attacks and death threats after he depicted the Prophet as a dog in 2007.
A Pennsylvania woman last year received a ten-year prison term for a plot to kill Vilks. In 2010, two brothers tried to burn down his house in southern Sweden and were imprisoned for attempted arson.
After Islamic militants attacked the Charlie Hebdo satirical magazine in Paris last month, killing 12 people, Vilks said that even fewer organisations were inviting him to give lectures over increased security concerns.
Vilks also said he thought Sweden’s SAPO security service, which deploys bodyguards to protect him, would step up the security around him.
“This will create fear among people on a whole different level than we’re used to,” he said. “Charlie Hebdo was a small oasis. Not many dared do what they did.”
Lars Vilks profile: Cartoonist has lived in fear since 2007
SWEDISH cartoonist Lars Vilks has been living under police protection since 2007 after his sketches depicting the Prophet Mohammed as a dog led to death threats from militant Islamists.
The controversial artist has amassed both fame and notoriety since the pencil drawings were published in a Swedish newspaper.
Some have heralded Vilks as a hero of free speech, but others have condemned him for his deliberate provocations, as Islamic law generally opposes any depiction of the prophet, even favourable, for fear it could lead to idolatry.
Vilks made his rough sketch showing Mohammed’s head on a dog’s body more than a year after 12 Danish newspaper cartoons of the prophet sparked furious protests in Muslim countries in 2006.
The drawing was turned down for an exhibition at the Sweden cultural heritage centre amid security concerns.
The issue went largely unnoticed until a Swedish newspaper printed the drawing with an editorial defending the freedom of expression.
Speaking to a journalist in Stockholm at the time, Vilks, 68, said: “I’m actually not interested in offending the prophet. The point is actually to show that you can.
“There is nothing so holy you can’t offend it.”
The publication led to protests from Muslim countries, and briefly revived a heated debate in the West and the Muslim world about religious sensitivities and the limits of free speech.
It also led to numerous death threats against Vilks, who was temporarily moved to a secret location after al-Qaeda in Iraq put a $100,000 (£65,000) bounty on his head in September 2007 – with an extra $50,000 if a knife was used.
The artist, who is given the highest threat rating from the FBI when he visits America, previously revealed he has built his own home defence system – including a “homemade” safe room and a barbed-wire sculpture that could electrocute potential intruders.
He also said he has an axe “to chop down” anyone trying to climb through the windows of his home in southern Sweden.
His home was hit by a suspected arson attack in 2010 and he has also been physically assaulted, and the victim of a failed assassination plot in 2009.
On 10 September, 2011, three men were arrested on suspicion of preparing to commit terrorist crimes in Gothenburg. Two days after the arrest, the crime classification was changed to conspiring to murder. It was revealed a few days later that Vilks was the intended target.