Jews believe Joseph's Tomb in the north of the Palestinian territory is the burial site of the Biblical patriarch Joseph. Muslims consider it the burial place of a local religious figure.

The entry of Jewish pilgrims often sparks clashes with Palestinians, who claim the visits are a provocation.

Thursday's prayer was exceptional as worshippers performed the Jewish morning service known as the Shacharit, which is celebrated after sunrise.

For a quarter of a decade, Israeli authorities have only allowed Jews to come and pray at the site at night.

"This is a significant and important step toward... ensuring the full return of the people of Israel and the State of Israel to this holy place," said Yossi Dagan, the head of the Shomron regional council which administers Israeli settlements in the northern West Bank.

"For the first time in 25 years, Jews prayed in broad daylight at Joseph's Tomb," the council said in a statement.

The tomb lies within the built up area of Nablus in the West Bank's Area A, which under the Oslo Accords signed in the 1990s falls under the administration of the Palestinian Authority.

Since the Israeli military vacated the site in 2000, Jewish pilgrims can only visit in groups escorted by troops.

AFP footage from the site on Thursday morning showed crowds of Jewish pilgrims praying, some wearing small leather boxes called tefillin, containing religious verses, on their heads.

The Israeli army has long supervised the entry of ultra-Orthodox Jews for a nighttime prayer on the first day of each month of the Hebrew calendar.

But Israeli media reported that, in December, Defence Minister Israel Katz had issued directives to the military to allow more visits to the tomb and not only at night.

Previously, buses of visitors escorted by the army had to leave the site by 4:00 am at the latest.

An AFP journalist at the scene said around 25 full buses arrived during the night carrying ultra-nationalists from Israeli settlements in the West Bank, as well as ultra-Orthodox Jews from settlements and from inside Israel.

The buses departed at 7:00 am, escorted by military vehicles, the journalist said.

Israel has occupied the West Bank since 1967 and Israeli settlements there are considered illegal under international law.

An Israeli military spokesperson told AFP that "all was done according to the orders of the political echelon, not an army initiative."

"The political echelon decided to extend the opening hours and (the military) is subordinate to their instructions."