Five Palestinians, including three teenagers, were killed while carrying out attacks Sunday, the latest in a wave of Palestinian knife, gun and car-ramming attacks on Israelis that erupted at the beginning of October.
Since then 172 Palestinians and 26 Israelis have been killed.
Most of the Palestinians were carrying out attacks but others died during clashes and demonstrations.
Malki pointed to ongoing Israeli occupation of the West Bank, which began in 1967, saying Palestinians born under it have seen nothing "but humiliation, soldiers' check-points, deaths and killing".
"They are born without any hope for the future... that's why sometimes they (teenage assailants) decide to sacrifice their lives even at the age of 15... for the better lives of the rest of the Palestinians," Malki told a press conference.
He is visiting Japan with Palestinian president Mahmud Abbas, who was due to meet Japanese Prime Minister Shinzo Abe later Monday.
Malki added that authorities do not advocate violence and are trying to prevent it.
"But the international community has to understand that there is a limit to everything," he said.
Signup to our newsletter and follow us on Facebook and Twitter!
Some analysts say Palestinian frustration with Israeli occupation and settlement building in the West Bank, the complete lack of progress in peace efforts and their own fractured leadership have fed the unrest.
Israel blames incitement by Palestinian leaders and media as a main cause of the violence.
Peace talks collapsed in April 2014 and since then, the situation has deteriorated, with the prospects of fresh dialogue appearing more remote than ever.
Malki said that one-on-one talks with Israel were out of the question.
"We will never go back and sit again in a direct Israeli-Palestinian negotiations."
He stressed that a multilateral framework to solve the Israeli-Palestinian conflict is needed and he praised an initiative discussed late last month by France to revive plans for an international conference to end the conflict.
And he warned that without international involvement a vacuum will be left that may end up being filled by the Islamic State jihadist group.
"If Daesh take advantage of lack of any brokers... then of course, they might come and try to fill it," he said, referring to Islamic State.
"This is very dangerous," he added.
"If the Americans are giving up and the Europeans don't have the courage to do anything and Arabs are really worried about their own problems, what do you expect? Extremists around might take over."