Tutu said he had asked Ismail Haniya, prime minister of Gaza's Hamas government: "Can you stop the firing of rockets into Israel?"
Haniya was dismissed by Mahmud Abbas, the Palestinian president, last June when Hamas seized control of Gaza from forces loyal to Abbas."The incident we are meant to investigate was a violation of human rights in the fact that civilians were targeted," he said.
"We have said to the prime minister [Haniya] that equally, what happens with rockets fired at Sderot is a violation."
Tutu was referring to the town in southern Israel that has borne the brunt of rocket and mortar fire by Gaza fighters.
He also condemned the blockade that Israel says it imposes in a bid to pressure the Hamas authorities to end the attacks by militants.
"What is happening in Gaza is unacceptable. We have already seen and heard enough to move us to tears," Tutu said after his 40-minute meeting with Haniya.
South African model
Tutu, who was a prominent anti-apartheid activist when South Africa was still under white minority rule, said it was crucial that the two sides negotiate.
"That was our experience in South Africa. Peace came when former enemies sat down to talk," he said.
On Wednesday, the team was due to visit Beit Hanoun, where the 2006 killings occurred, to interview witnesses and survivors of the attack.
They will prepare a report to present to the UN Human Rights Council in Geneva.
The Israeli attack on Beit Hanoun on November 8, 2006, was widely condemned by the international community for killing 19 civilians, including five women and eight children, in their homes.
Owen Fay, Al Jazeera's correspondent in Gaza, said Israel and the Palestinians remained at odds over what happened in the Beit Hanoun attack.
"In the aftermath of the attack the Israelis conducted an internal investigation [and] concluded that they were at fault and that there was something wrong with the launch mechanism of the rockets that they fired in," he said.
"They offered some financial compensation and they did apologise, but frankly the neighbours and the family members themselves have never really accepted the Israelis' explanation.
"They say the number of rockets that were fired were double the number that Israel claimed. They also said that as they moved further away from the house that had been , the rockets came in and attacked them. They feel that they were very deliberately targeted."
The Israeli army announced in February that no charges would be brought against Israeli soldiers over the attack.
Also on Wednesday, two Hamas fighters were killed and one injured in an Israeli air raid east of the Gazan town of Rafah.
The Israeli military says the attack was aimed at Palestinian fighters armed with mortars who were approaching Israeli forces in the area.
Hamas said that 26 mortar rounds were fired at the Israeli soldiers.