Wallstrom was responding to a question in parliament by an opposition member on the controversy raised in December by her statement on the need for Israel to avoid "extrajudicial executions".
She was referring then to the more than 100 Palestinians killed in two months, most while committing or attempting to commit knife attacks in Israel and the Palestinian territories, and others in clashes or attacks.
Since then the Palestinian toll has reached 149, including an Israeli Arab.
"It is essential that thorough and credible investigations be conducted concerning these deaths with the aim of providing clarity and bringing about possible accountability," Wallstrom said Tuesday.
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Israel's foreign ministry responded angrily.
"In her irresponsible and delusional statements the foreign minister of Sweden gives support to terror and in so doing encourages violence," it said in a Hebrew-language statement.
Ties between Israel and Sweden plummeted after Stockholm recognised the Palestinian state shortly after Wallstrom's centre-left Social Democrats won a parliamentary election in 2014.
A day after the Paris attacks claimed by the Islamic State group, Wallstrom again attracted Israeli condemnation when she said the decades-old Israeli-Palestinian conflict was a factor in radicalisation.
The Israeli foreign ministry said then that Wallstrom "has consistently demonstrated bias against Israel".