There were angry scenes as boos broke out and people shouted at Manuel Valls when he arrived at the Monument du Centenaire ahead of a minute’s silence.
Families of the dead and injured gathered alongside emergency services, who were applauded and thanked by members of the crowd.
Following the silence, for which thousands of people flocked to the Promenade des Anglais, there was applause and a rendition of the French national anthem as many of those singing defiantly raised their fists in the air.
Mr Valls was booed again as he walked to a nearby garden where flowers were laid in tribute.
Eighty-four people were killed when Mohamed Lahouaiej Bouhlel drove a hired lorry through crowds gathered to celebrate Bastille Day on Thursday.
The French-Tunisian father of three was killed by police after his rampage.
On Monday people threw rubbish on the spot where he was shot in a bid to show their disgust.
Explaining the anger towards Mr Valls, one French woman said people feel a stronger prime minister is needed as the country tries to defeat extremism.
Nice resident Isabel, who declined to give her surname, said she did not boo but understood why tensions are running high.
“They want him (Mr Valls) to resign because he didn’t put enough police on on the day,” said the 60-year-old. “I was there (on Thursday) and didn’t see police.
“It’s terrible to say but we need a stronger prime minister with laws against radicalism.
“I am very sad. It (the attack) has broken families apart for nothing.”
The city’s former mayor Christian Estrosi has said he asked for extra security ahead of the Bastille Day celebrations but was refused.
Eighteen of the 85 people still in hospital are in a life-threatening condition, the country’s health minister said on Sunday.
There has also been anger at the length of time it is taking to identify victims.
So far 35 bodies have been identified, and 12 more are due to be presented to families on Monday, said the secretary of state in charge of help for victims, Juliette Meadel.
With France into its third day of national mourning, information about driver Bouhlel continues to emerge.
He had scouted out the promenade before the attack, CCTV footage showed, and he is said to have sent texts to possible accomplices asking for more weapons.
A police official would not confirm the reports, but it is believed one of the eight people detained during the investigation had received messages from the 31-year-old.
Seven people remain in custody following arrests during the weekend.
Bouhlel is believed to have been radicalised recently, with former neighbours saying they were shocked by his actions. They claimed he was not a devout Muslim and could not have been an extremist who Islamic State (IS) described as one of its “soldiers”.
Bunches of flowers and candles left on the promenade, many at the exact spots where people were killed, have swelled in number.
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