Israelis have held a series of demonstrations in recent weeks calling on Mr Netanyahu to resign, citing his trial on corruption charges and his fractious unity government’s poor handling of the coronavirus pandemic.
The protest near the prime minister’s residence began around sundown on Thursday and was initially largely peaceful but police said at least 55 people were later arrested.
A smaller counter-protest in support of Mr Netanyahu was held nearby, with the two camps separated by metal barricades and a large police presence.
Police say they moved in to disperse the protesters when they tried to stage a procession through the city.
Officers scuffled with demonstrators before four large trucks roared into action, spraying water cannons and scattering the protesters.
At times, it appeared the trucks were spraying protesters from behind as they tried to leave the area peacefully.
Israel imposed a general lockdown when the first coronavirus cases appeared in March and by May had largely succeeded in containing the outbreak. But then it moved quickly to lift virtually all restrictions, and in the following weeks cases surged.
The country has reported a total of more than 57,000 cases and at least 442 deaths. More than 24,000 patients have recovered.
A unity government formed in May following three inconclusive elections in less than a year was supposed to prioritise the pandemic. Instead, it has been plagued by infighting and unable to agree on clear policies to combat the pandemic.
Mr Netanyahu meanwhile faces charges of bribery, fraud and breach of trust over a series of long-running corruption investigations.
Critics say he is more focused on escaping legal accountability than on containing the pandemic. Many have speculated he intends to call yet another election, allegations he dismissed as “absurd” in a Thursday press conference.
At the same conference, held as the protests were under way, he called on demonstrators not to clash with police, saying it would “lead to anarchy”.