The demonstrations on Sunday came after long-running efforts to broker a truce gained momentum last week when Hamas dropped a key demand for an Israeli commitment to end the war.
The militant group is still seeking a permanent ceasefire, while Netanyahu has vowed to keep fighting until Hamas is destroyed.
The war was triggered by Hamas' cross-border attack on October 7, in which 1200 people were killed and 250 others taken hostage.
Israel's retaliatory offensive has killed over 38,000 Palestinians, according to the territory's Health Ministry, which does not distinguish between combatants and civilians in its count.
Israelis launch 'Day of Disruption'
Sunday's "Day of Disruption" started at 6.29am (1.39pm AEST), the same time Hamas militants launched the first rockets toward Israel in the initial attack. Protesters blocked main roads and demonstrated outside of the homes of government ministers.
Near the border with Gaza, Israeli protestors released 1500 black and yellow balloons to symbolise those fellow citizens who were killed and abducted.
Hannah Golan said she came to protest the "devastating abandonment of our communities by our government".
"It's nine months today, to this black day, and still nobody in our government takes responsibility," she said.
About 120 hostages remain captive after more than 100 hostages were released as part of a November ceasefire deal. Israel has already concluded that more than 40 of the remaining hostages are dead, and there are fears that the number will grow as the war drags on.
The US has rallied the world behind a proposal for a phased ceasefire in which Hamas would release the remaining captives in return for a lasting ceasefire and the withdrawal of Israeli forces from Gaza.
But Hamas wants guarantees from mediators that the war will end, while Israel wants the freedom to resume fighting if talks over releasing the last batch of hostages drag on.
Netanyahu has also said Israel is still committed to destroying Hamas' military and governing abilities, and that it would resume the war after a pause to release hostages.
Israel continues to battle pockets of Palestinian militants across Gaza after months of heavy bombing and ground operations that have devastated the territory's major cities and driven most of its population of 2.3 million people from their homes, often multiple times.
Bodies found with hands tied
The Nasser Hospital in the southern Gaza town of Khan Younis said the bodies of three Palestinians were retrieved from the area of the Kerem Shalom crossing with Israel.
A hospital statement said they were handcuffed, and an Associated Press reporter saw one of the bodies with bound hands.
Abdel-Hadi Ghabaeen, an uncle of one of the deceased, said they had been working to secure the delivery of humanitarian aid and commercial shipments through the crossing. He said he saw soldiers detain them on Saturday, and that the bodies bore signs of beatings, with one having a broken leg.
The Israeli military said it was looking into the reports.
Thousands of Palestinians have been detained since the start of the war, and many of those who have been released, as well as some Israelis who have worked at detention facilities, say detainees have been tortured and held under harsh conditions. Israeli authorities have denied abusing prisoners.
Israeli airstrikes overnight and into Sunday meanwhile killed at least 13 Palestinians, according to Palestinian officials.
Six were killed in a strike on a house in the central town of Zawaida, according to the al-Aqsa Martyrs Hospital.
A strike on a school-turned-shelter in Gaza City killed four people, and a strike on a house near the city killed three, according to the Civil Defence, a first responders group under the Hamas-run government.
Civilians flee in Rafah as Israel pushes ahead with its offensive
Israel trades fire with Hezbollah
The Lebanese militant group Hezbollah said on Sunday that it launched dozens of projectiles toward northern Israel, targeting areas more than 30 kilometres from the border, deeper than most launches.
A 28-year-old man was seriously wounded, Israel's national rescue service reported. The barrage came after an Israeli airstrike killed a Hezbollah militant on Saturday.
Hezbollah began launching rocket and mortar attacks after the outbreak of the war in Gaza.
The range and severity of the attacks and Israel's counterstrikes have escalated in recent weeks, raising fears of an all-out war that would have catastrophic consequences for people on both sides of the border.
Mediators from the US, Egypt and Qatar have intensified their efforts in the past week to broker an agreement between Israel and Hamas. Hezbollah has said it will halt its attacks if there is a ceasefire in Gaza.
The compromise on Saturday by Hamas could lead to the first pause in fighting since November and set the stage for further talks, though all sides still warned that a deal is not yet guaranteed.
Washington's phased deal would start with a "full and complete" six-week ceasefire during which older, sick and female hostages would be released in exchange for hundreds of Palestinian prisoners.
During those 42 days, Israeli forces would withdraw from densely populated areas of Gaza and allow the return of displaced people to their homes in northern Gaza.
War-weary Palestinians in the Gaza Strip appeared pessimistic, after previous instances in which the two sides appeared to be closing in on a deal.
"We have lived nine months of suffering," said Heba Radi, a mother of six children living in a tent in the central city of Deir al-Balah, where she has been sheltering since they fled their home in Gaza City.
"The ceasefire has become a distant dream."
