The new Commissioner-General of UNRWA Pierre Krahenbuhl pledged to defend Gaza and to work hard to end the blockade.
Six Palestinian were detained inside the Al-Aqsa compound, amid tensions as Jewish groups attempt to hold Passover rituals in al-Aqsa.
A five-member delegation commissioned by Mahmoud Abbas have arrived in Gaza to discuss reconciliation with Hamas.
Stark warning follows reports Palestinian president may disband Palestinian Authority if talks end by 29 April without extension.
Announcement follows similar decisions by authorities in Argentina and Netherlands - Actions against Mekorot held across 12 countries.
Dozens of Palestinian worshipers were wounded and dozens were detained after clashes broke in the Al-Aqsa Mosque compound.