Witnesses told Ma’an the settlers first arrived in groups at midnight and performed prayers while dancing and shouting, disrupting the community throughout the night. They left the town at 7 am.
The settlers also affixed posters with religious slogans in Hebrew on walls in several parts of the town.
An Israeli army spokesperson said they were looking into reports.
A number of tombs exist in Kifl Haris, which Palestinians in the area believe to be the graves of the prophet Dhul-Kifl, the Sufi saint Dhul-Nun, and another shrine built by 12-century sultan Saladin.
However, some Jews believe the tombs belong to the biblical figures Joshua, Caleb and Nun.
Like many other Palestinian towns across the West Bank with religiously significant sites, Kifl Haris, situated on the main road connecting the illegal Ariel settlement to Jerusalem and Tel Aviv, commonly experiences incursions by Israeli settlers accompanied by armed escorts.
Settlers who visit the tombs to pray often actively disrupt Palestinian residents and damage property.
Meanwhile, Palestinians are restricted from visiting holy sites in Israel without hard-to-obtain permits from Israeli authorities.
Tasnim News Agency - world