"This is the first time I received my complete salary in more than a year," Jasser Sbai, an agriculture ministry employee in the West Bank city of Ramallah, said.
"Unfortunately most of this salary will go to the electricity company and shops because I owe them too much," he added, surrounded by more than 50 Palestinians waiting to use the cash machine.
Ruba Hamad, who has an entire year's rent payment outstanding, said: "The problem is how to solve what happened in previous months. We need another month's salary to cover all of our debts."
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The salary payments will be a boost to the emergency government sworn in by Mahmoud Abbas, the Palestinian president, after he dismissed the Hamas-led unity government, which took control of the Gaza Strip last month.
Officials have not said how many Palestinians would receive their pay cheques on Wednesday, but the Hamas movement in the Gaza Strip said that up to 23,000 civil servants will miss out because of their links with the group.
"The Fayyad [the new prime minister] government's decision not to give thousands of employees their salaries enforces the political and geographical separation of Palestinian people," Sami Abu Zurhi, Hamas spokesman, said.
Hamas has not said whether its administration which effectively controls the Gaza Strip would take any steps to pay those workers.
Members of the Fatah-dominated security services in Gaza have been asked by their commanders in the West Bank to stay at home as a condition for receiving their salaries.