The protest has been underway for several days and was sparked by severe cuts to the UNRWA budget due to the suspension of 300 million dollars in US funding.
Palestinian police followed the protestors at a distance, simply ensuring that they did not force their way into the offices.
In an interview with the WAFA news agency, Mathias Shamali, UNRWA chief in Gaza, said that 145 of the about 1,000 employees on short-term contracts had been laid off as part of the cuts.
He noted that the population in the Gaza Strip is "very anxious out of concern that more measures could be brought in soon".
The biggest worry, he said, is about the reopening of the 275 schools run by UNRWA in Gaza that may not open in late August as scheduled.
UNRWA has said that it is seeking other funding to compensate at least in part of the funds lost from the US.
The Swedish government has pledged to donate 60 million dollars per year, while the EU is expected to donate 80 million euros.
However, even if this happens not all the funds will be replaced.