Palestinian Authority Prime Minister Ismail Haniya's convoy was attacked by gunmen at the Rafah border crossing, killing a bodyguard and wounding five people including Haniya's oldest son.
The violence late on Thursday capped a day of chaos at the Rafah crossing, where Haniya waited most of the day to enter from Egypt to Gaza, carrying $35 million in cash.
Palestinian Authority Foreign Minister Mahmoud al-Zahar blamed the attack on militants from the rival Fatah movement of President Mahmoud Abbas.
Palestinian eyewitnesses said that militants guarding Haniya's convoy fired first on Abbas' security officials, who guard the Rafah crossing.
The witnesses said the presidential guards responded to the fire, killing a bodyguard and injuring five, including Abul Sallam Haniya.
"We know very well who opened fire at our convoy, which caused some casualties, and we know very well how to react to it," Haniya said after the shooting.
Al-Zahar said several officials from the Hamas movement and the Hamas-led Palestinian Authority cabinet departments were at the crossing to receive Haniya.
"None of us carried any arms. On our way out, suddenly, unknown militants fired at the convoy," he added.
Al-Zahar called on Abbas to immediately open an investigation "to know who the people are and why they opened fire at the prime minister's convoys".
Earlier Thursday before entering Gaza, Haniya was forced to leave behind an estimated $35 million he had collected abroad, security sources reported.
Haniya's entry to the Gaza Strip was delayed for several hours after Israeli Defence Minister Amir Peretz ordered his forces to close the Rafah crossing and block Haniya from carrying the money into Gaza.
The closure triggered a struggle at the crossing, where dozens of armed Hamas supporters stormed the crossing on the Gaza-Egypt border, witnesses reported.
Haniya had to cut short his two-week foreign trip after Jordan, Saudi Arabia, Oman and Lebanon refused official meetings with him, government sources said. But he visited Iran and several Arab countries.
Palestinian ministers and officials have previously returned from trips abroad with millions of dollars in cash in an attempt to circumvent the political and economic boycott imposed on Haniya's government because of its refusal to recognise Israel.
Israeli political sources said Israel agreed to allow Haniya to cross from Egypt into the Gaza Strip on the condition that he could not bring in large sums of money.
"It was agreed with President Mahmoud Abbas that Prime Minister Ismail Haniya leave the money in Egypt and enter into Gaza without it.
The money then would be legally transferred to the government," said Ghazi Hamad, spokesperson of the Hamas-led cabinet.
"It was agreed to transfer the money either to Palestinian banks and then into the Finance Ministry's account, or through the Arab League.
This money is to help the Palestinian people, who suffer from severe economical crisis."