Mr Kerry said the prospect of a peace deal based on a two-state solution was in grave jeopardy.
Israeli settlement building on occupied land was a major problem, he said.
Mr Netanyahu said he was disappointed with the speech, which he said was “unbalanced” and “obsessively focused” on settlements.
Mr Kerry had “paid lip service to the unremitting Palestinian campaign of terrorism” against Israel, he said
He added that the conflict centred on the Palestinians’ refusal to recognise Israel’s right to exist, but Mr Kerry “does not see the simple truth”.
Earlier, US President-elect Donald Trump saying he would not allow it to be treated with “disdain and disrespect”.
He urged Israel to “stay strong” until he assumed office next month.
On Friday, the US chose not to veto a UN Security Council resolution calling for an end to Israeli settlement construction, leading to an angry response from Israel.