Scuffles have broken out between Palestinian civil servants in the Gaza Strip after those linked to Hamas found out they had not been paid.
Police had to separate them from Fatah workers and cash machines were closed down.
The Palestinian Authority insisted the Hamas employees would have to be vetted before they received their salaries.
A Palestinian unity government was sworn in on Monday, a key step towards ending the rift between the two sides.
The two factions had governed separately since Hamas, which won elections in 2006, ousted Fatah from Gaza in 2007.
Civil servants employed by Hamas hoped to receive salaries from the West-Bank based Palestinian Authority on Thursday.
Several reacted with anger when it transpired that their salaries had not been paid into their accounts, while those of their Fatah colleagues in Gaza had.
Fist fights and scuffles reportedly broke out near banks and cash machines, which were then closed in order to prevent further violence.
Hamas spokesman Sami Abu Zahri told AFP that "discrimination" had taken place.
"The new government must take responsibility for everyone, and not take steps that will bring back the division of before", he said.
Qatar steps in
The deputy chief of Hamas, Ismail Haniyeh, said that he had secured a pledge from the leader of Qatar to temporarily fund the payments.
Qatar is a key supporter of the Muslim Brotherhood, the Islamist group from which Hamas originated.
The new government comprises 17 politically independent ministers and must organise elections to be held within six months.
Israel has insisted it will not deal with a Palestinian government backed by Hamas. Along with the US, it considers Hamas a terrorist group.
On Thursday Israel announced a plan for almost 1,500 new homes in the occupied West Bank.