The protests have been sparked by corruption allegations against Netanyahu, who denies any wrongdoing.
Violence erupted for a third day in Gaza in response to President Donald Trump’s announcement on Wednesday, which overturned decades of US policy towards the Middle East.
India’s response was muted, with no reiteration of its long standing position on East Jerusalem being the future capital of Palestine.
On the last two days of the UNHRC session, India voted in 15 resolutions and made a statement on Myanmar, the only resolution that did not go to a vote.
The visit will mark 25 years of diplomatic relations with Israel and will be the first time an Indian leader will skip visiting neighbouring Palestine.