Religious Endowments Authority (Al Waqf) director Sheikh Abdul Azim Salhab was arrested early on Sunday as part of an overnight raid carried out by Israeli forces in the occupied West Bank and Jerusalem, Mahdi Abdelhadi, a senior member of Al Waqf, said.
At least 13 other Palestinians were also arrested, including Salhab's deputy, according to Maan news agency.
"He's the most senior Jordanian figure in the (Palestinian) territories. 20 years ago (if) the police wanted to interrogate the mufti, they would call and invite him, but coming to a 75-year-old's home like that at 5 am is unacceptable," the official was quoted as saying.
The head of Jordan's Ministry of Al Waqf and Islamic Affairs strongly condemned Salhab's arrest, the report added.
Abdulnasser Abu al-Bassal accused Israel of "playing with fire amid difficult circumstances".
He also described a warrant issued against Sheikh Azzam al-Khatib in Jerusalem, head of the Al Waqf, as an unacceptable escalation that affects Jordan's role as the custodian of holy sites in Jerusalem.
Al-Bassal called for the release of those imprisoned and for the cancelation of al-Khatib's warrant.
The arrest comes after Palestinians on Friday prayed at an area by the Al-Rahma gate, located inside occupied East Jerusalem's Al-Aqsa Mosque complex, for the first time in 16 years.
It is a passageway of gates and a stairway leading to a hall that had been closed by Israeli authorities for years, and was reopened on Friday by Muslim religious officials. The hall is located a short distance from Al-Aqsa Mosque itself.
The Israeli authorities closed the area in 2003. In 2017, an Israeli court upheld the closure order.