France is now in a state of emergency due to other terror attacks that have plagued the country as of late.
The motive for the attack was unclear, but the Paris prosecutor's office, which handles terrorism cases nationwide, said on Sunday that it had opened a terrorism investigation.
French interior minister Gerard Collomb has said he will travel immediately to the scene.
About 40 minutes later police said in a second tweet that the attacker had been "neutralized and shot".
Police in the city warned of and ongoing situation at the station at around 1.30pm (British summer time) and had told people to tay away from the area. The attacker allegedly shouted "Allahu Akbar" during the attack.
The attack at Marseille's busiest train station took place early this afternoon, as scores of armed police officers and soldiers swarmed the area.
"The presence of Sentinelle soldiers, their speed and efficiency ensured that the death count was not bigger", police union official Stephane Battaglia told Reuters.
The incident in Marseille came only days after the Daesh group released a recording of what it said was its leader Abu Bakr Al Baghdadi urging his followers to strike their enemies in the West.
Since November 2015, the country has been in a state of emergency which gives the government and security forces greater powers to combat extremists and launch anti-terror raids.
President Emmanuel Macron said on Twitter he was "disgusted by this barbaric act" and praised the calmness and efficiency of security forces.
This incident comes weeks after four Boston College students were attacked with acid at the same train station.
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