Israeli Housing Minister Uri Ariel, deputy leader of the hardline national religious Jewish Home party, briefly visited the plaza in al-Quds on Sunday.
After the visit, clashes broke out between stone-throwing Palestinian youths and Israeli police at the site, police spokeswoman Luba Samri told AFP.
"Jordan rejects Israeli escalation in Al-Aqsa as well as measures that allow radicals to violate Al-Aqsa under protection of police and occupation forces," Minister of Information Mohammad Momani said in a statement carried by state-run Petra news agency on Monday.
"These actions will lead to more violence and religious extremism in the region. Jordan warns Israel not to try to impose anything new related to Al-Aqsa."
By law, Jews are not allowed to pray at the site and such high-profile visits by rightwing government figures are very rare and tend to stoke tensions.
Under the 1994 Israeli-Jordanian peace treaty, the kingdom is allegedly the custodian of Muslim holy sites in occupied al-Quds.
Last month, Jordanian Prime Minister Abdullah Nsur warned Amman might review the peace deal after the Zionist regime’s MPs debated allowing Jewish prayers at Al-Aqsa mosque compound.
NJF/NJF