"If you have to use live ammunition, why couldn't you shoot them in the legs?"
"Why did you have to kill them to stop them scaling the fence?"
Mr Netanyahu claimed terror group Hamas had organised the protests to maximise casualties because they knew that dead bodies "photograph better".
He added: "Everything you said Mr Howard has been tried and other things and it didn't work and in fact nobody intentionally went out to kill anyone. People died accidentally.
"And I can tell that you that Hamas at a certain point said 'not enough people have been killed, push more, let the Jews kill more.'
"Their goal was to maximise casualties, our goal was to minimise casualties and avoid fatalities. This is a new tactic. It's a new form of warfare."
After the confrontation, Lord Howard said he was not satisfied with the Israeli PM's explanation.
He said: “We have dealt with situations, not exactly the same, but we have dealt with situations in Northern Ireland without using force and when we did use force on Bloody Sunday, we learnt form that.”
During his talk, Mr Netanyahu claimed Israel had been trying to find a way to deal with protests such as those on the Gaza border without having to use live ammunition.
He said: "We tried water cannons and tried tear gas and none has worked against this kind of tactic so they're working on it and given our record we probably will figure out something, but we haven't got there yet.
"We're investing in this very heavily now."
Speaking at the event, hosted by think tank Policy Exchange, Mr Netanyahu said the nuclear deal signed by the UK and other European nations with Iran was "effectively defunct" and he urged others to follow the lead of US President Trump by tearing up the 2015 agreement.
He also attacked the failure of UK government to proscribe Hezbollah as a terrorist organsation because of an alleged difference between the Iranian led group's political and military wings.
This distinction creates a legal loophole that allows people to fly the group's flag on political grounds, as they have at the annual Al Quds Day Parade in London, the next of which is on Sunday.
He said: "They are seeking the destruction of not only Israel but also Jews."
