Four police officers are standing by their car parked outside the grand synagogue in Marseille, a short walk from the city's old port. They watch as worshippers slip inside through a side door.

"It's normal," said one, as he held open the door, referring to the police presence. "You can't help people being worried."

The officer was referring to the possibility of another antisemitic attack following the deadly shootings by a suspected French jihadist at the Jewish museum in Brussels on 24 May. Ninety synagogues and Jewish schools in Marseille have been placed under police guard since the attack in the Belgium capital, which killed four people. The French city's 80,000-strong Jewish community has had no alternative other than to "bunkerise", said Michèle Teboul, the leader of a regional Jewish organisation.

French police have been taking no chances since the chance arrest of the suspect in the Brussels attack, Mehdi Nemmouche, at bus station in the Marseille: the adjacent Saint-Charles railway station was evacuated during last Friday's rush-hour after the discovery of a suspicious package.

The Jewish museum attack has focused attention on the threat from an estimated 780 French jihadists returning from the war in Syria, and investigators' difficulties in tracking them. Nemmouche is suspected of carrying out the attack after returning from Syria via a circuitous route through Asia.

The French prime minister, Manuel Valls, who was interior minister until March, said the threat of the returning European jihadists was on an unprecedented scale and was "without a doubt, the greatest danger that we must face in the coming years".

Nemmouche's arrest on 30 May was a wake-up call, said the deputy mayor of Marseille, Nora Preziosi, a politician who hails from the city's inner city northern districts, which carry a reputation for violent crime linked to drug-dealing and cigarette smuggling.

"My beautiful religion is being sullied," said Preziosi, a member of the centre-right UMP party and an admirer of the former president Nicolas Sarkozy, whose photographs adorn her office. "The vast majority of Muslims are republican, they are against what is happening. Islam is being sullied by the Salafists, and stigmatised by the media."

Referring to Nemmouche, she added: "What was he doing in Marseille? He should have been followed. These people should be placed under surveillance, that's the state's responsibility."

Camille Hennetier, a deputy prosecutor in charge of the central investigative anti-terrorist unit in Paris, points out that France has aggressive legislation that permits the arrest of people suspected of being part of a criminal conspiracy plotting terrorist acts. "It's not a crime to be radical," she said. "But it is a crime to wage jihad."

French police have pre-emptively arrested a number of people suspected of being jihadists, including 21 people over the past 18 months linked to a group with Syria connections known as the "Cannes-Torcy" cell. Six alleged jihadist recruiters were detained last week after Nemmouche's arrest. But Hennetier's colleague, general prosecutor Ludovic Lestel, said investigators were hampered by the jihadists' use of social media and Skype, which are more difficult to monitor than extremist websites.

French authorities recently publicised a free hotline for family members to come forward with concerns about extremists in their midst. But 75% of the calls so far have been abusive.

The sheer number of potential terrorists is also a challenge for investigators. About 90 violent extremists returned from Afghanistan, compared with the current surge of French nationals who take cheap flights to Turkey, where the men leave their wives and children before heading across the border. According to the interior minister, Bernard Cazeneuve, 285 jihadist fighters are now in Syria – a 75% increase compared with the previous six months. President François Hollande said last week that 30 French nationals had been killed in the Syrian civil war.

Marseille, a city where one in four of the 850,000 population is Muslim, poses no significant jihadist threat compared with other cities, according to Lestel. He identified Toulouse – where Islamist Mohamed Merah went on a murderous rampage two years ago before being killed in a police siege – the Paris region, and northern France as the zones where the majority of investigations targeting suspected home-grown jihadists were being pursued.

Marseille-Espérance was set up in 1990 by the city's then mayor, Robert Vigouroux, a Socialist, to preserve the fragile social harmony in the city whose places of worship are often cheek by jowl. Co-founder Salah Bariki pointed out that Marseille escaped the explosion of rioting that hit the crime-ridden impoverished suburbs of other French cities in 2005.

Marseille-Espérance works behind the scenes to bring together the religious leaders from the Muslim, Jewish, Armenian, Greek orthodox and Buddhist communities, who meet twice a year with the centre-right mayor, Jean-Claude Gaudin.

"We don't talk about religion," Bariki said, "and we don't do politics."