People of Israel held a series of demonstrations in recent weeks calling on Netanyahu to resign and demanded his trial on corruption charges.
They blamed the PM for his fractious unity government’s poor handling of the coronavirus pandemic.
The protest near Netanyahu’s residence began around sundown on Thursday and was initially largely peaceful.
However, a smaller counter-protest in support of Netanyahu was also held nearby, with the two camps separated by metal barricades and a large police presence.
Police said that they moved in to disperse the protesters when they tried to stage a procession through the city.
Police scuffled with demonstrators before four large trucks roared into action, spraying water cannons back and forth, scattering the protesters.
The first coronavirus cases appeared in March and by May, Israel imposed a general lockdown. The country also moved quickly to lift virtually all restrictions, and in the following weeks Covid-19 cases surged.
Israel has reported more than 57,000 cases and 442 deaths until now.
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.
Meanwhile, Israeli Prime Minister faced charges of bribery, fraud and breach of trust over a series of long-running corruption investigations. Critics said he is more focused on escaping legal accountability than on containing the pandemic.
Many speculated that Israeli PM intends to call yet another election, allegations he dismissed as “absurd” in a Thursday press conference.