"The investigation has no moral ground since it decided even before it started who is guilty and of what," Yigal Palmor, a foreign ministry spokesman, said earlier this month.
Human rights groups have called for the UN investigation to look into allegations that the Israeli fired imprecise artillery and controversial white phosphorus shells in built-up neighbourhoods.
It is also expected to examine the indiscriminate firing of rockets into southern Israel by Palestinian fighters, Israel's stated reason for launching the offensive last December.
Sporadic rocket fire into Israel has continued since the war, and on Thursday Israel bombed a house in a Gaza refugee camp. No casualties were reported.
Goldstone's four-member team is expected to travel to the region in a few weeks' time and will issue a report to the council in July.
But Israel's refusal to work with the investigators raises questions about whether an adequate investigation can be completed.
However, Israel said that Goldstone, who is Jewish and has close ties to Israel, was not the problem.
"[It's] not about Justice Goldstone," Aharon Leshno Yaar, the Israeli ambassador to UN organisations in Geneva, said on Tuesday.
"It's clear to everybody who follows this council and the way that it treats Israel that justice cannot be the outcome of this mission."
In New York, a leading human rights group urged both sides to co-operate.
Human Rights Watch noted that it has criticised the UN rights council in the past "for its exclusive focus on Israeli rights violations".
However, Goldstone has the "experience and proven commitment to ensure that this inquiry will demonstrate the highest standards of impartiality," the group wrote in a letter to Hillary Clinton, the US secretary of state, and 27 European foreign ministers.
Hamas has already welcomed the investigation.
The investigators "will find full co-operation of the Palestinian government and Palestinian people because the crimes of the occupation are clear and no one can underestimate them", Yousef Rizka, an adviser to Ismail Haniya, the de facto prime minister in Gaza, said.
Israel is co-operating with a separate investigation into several attacks on UN facilities during the conflict, including one which destroyed a warehouse belonging to the UN Relief and Works Agency, which provides food aid for the Gazans.