Angry protesters threw shoes at UN chief Ban Ki-moon as he visited the Gaza Strip on Thursday, condemning him for failing to meet the families of Palestinian prisoners.

Ban was pelted as he crossed into the Palestinian territory, where a crowd of around 50 demonstrators tried to block his convoy as it entered Gaza.

As some threw sand and stones in addition to footwear, others toted pictures of imprisoned Palestinians and signs in English reading "Ban Ki-moon, enough bias for Israel."

Ban's convoy was able to proceed to Khan Yunis in southern Gaza, but further demonstrations met him there at stops at a school and a Japanese-funded housing project, with protesters holding banners saying "We demand a trial for Israel's leaders."

And a group of local NGOs and businessmen announced they were boycotting a planned lunch with the UN leader after his staff refused to allow them to bring some relatives of Palestinian prisoners in Israeli jails to the meeting.

A statement signed by some of Gaza's most prominent rights activists and businessmen said they had made "intensive efforts" to ensure relatives of Palestinian prisoners could meet Ban.

"We received an unjustified negative response indicating that the secretary general refused to meet with representatives of families of prisoners," the statement said.

The group expressed "strong dissatisfaction" with Ban's decision, noting that he had met on multiple occasions with the family of an Israeli soldier who was captured by Gaza militants in 2006 and held incommunicado for five years.

Ban released a statement on the demonstrations after he crossed back into Israel, saying he was "concerned about the situation of Palestinian prisoners in Israeli jails."

"The United Nations continues to call on Israel to abide by its obligations under international law," he said, without adding further details.

There are more than 5,000 Palestinians in Israeli prisons, and Palestinian officials in the West Bank and Gaza have raised concerns about the conditions in which they are held.

In a statement on Thursday afternoon, the executive committee of the Palestine Liberation Organisation apologised "for the behaviour, condemnable and alien to our traditions, to which UN Secretary General Ban Ki-moon was exposed."

The committee "reaffirmed its great respect" for Ban, citing his "large role in supporting Palestinian national rights."

Ban's visit to Gaza, part of a trip to Israel and the Palestinian territories, came hours after a barrage of eight rockets was fired from the coastal territory into southern Israel.

UN security decided to go ahead with the trip, but Ban strongly condemned the rocket fire, calling it "unacceptable."

"People from Gaza must stop firing rockets onto the Israeli side," he said at a news conference in Khan Yunis.

The UN chief also called on Israel to ease its restrictions on Gaza.

Israel limits imports and exports from the territory, citing security concerns and the need to deny access to weapons and money to the ruling Hamas, which it considers a terrorist organisation.

But much of the international community, including the United Nations, believes that the restrictions unfairly affect Gaza's entire population.

"Israel has taken some measures to ease the closure. More must be done," Ban said.

"I am pressing hard for policy changes so that the United Nations can do its essential work," he added, calling for Gaza to be able to trade "without restrictions."

Ban's trip to Gaza comes as part of a visit to Israel and the Palestinian territories intended to convince the two sides to continue meeting, as the international community seeks a way to kick-start direct negotiations.

In a Thursday night speech at a security conference in Herzliya, near Tel Aviv, Ban called on the sides "to return to negotiations. Not just procedural talks but substantive negotiations."

"Now is the time for demonstrations of good will on both sides," he added.

Ban arrived in the region shortly after five rounds of so-called exploratory meetings between Israeli and Palestinian negotiators ended without an agreement on a path back to direct talks, which have been on hold since September 2010.

On Wednesday, Ban urged Israel to offer the Palestinians "goodwill gestures" to lure them back to talks, amid reports that the international community wants the Jewish state to offer a package of confidence-building measures.

On Thursday, US envoy to the Middle East David Hale held talks with Palestinian president Mahmud Abbas, though no details of their discussions were made public.