The Al-Aqsa Foundation for Endowments and Heritage said that, from Sunday to Thursday, 407 Israelis – protected by Israeli police – had conducted individual and group tours inside the mosque complex.
Of these, 52 were young Israeli troops who entered the complex in military uniform as part of a so-called "guidance and exploration" program, the NGO said.
"Occupation forces harassed Muslim worshippers at the gates of the mosque complex, arresting 20 over the past week," it added.
It went on to say that detained worshippers had been subsequently released after being subject to monetary fines and barred from entering the Al-Aqsa complex for periods ranging from two weeks to one month.
Israeli officials could not be reached for comment on the issue.
Jewish settlers frequently force their way into the religious site through the Al-Magharbeh Gate.
A number of Jewish groups had called on supporters to storm the mosque compound this week to mark the advent of the Jewish Hanukkah holidays, or "Festival of Lights."
For Muslims, Al-Aqsa represents the world's third holiest site. Jews, for their part, refer to the area as the "Temple Mount," claiming it was the site of two Jewish temples in ancient times.
Israel occupied East Jerusalem during the 1967 Middle East War. It later annexed the holy city in 1980, claiming it as the capital of the self-proclaimed Jewish state in a move never recognized by the international community.
In September 2000, a visit to Al-Aqsa by controversial Israeli politician Ariel Sharon sparked what later became known as the "Second Intifada," a popular uprising against Israel's decades-long occupation in which thousands of Palestinians were killed.