The video, filmed by a local activist, has stirred Palestinian anger.
The video was said to have been taken yesterday after a 20-year-old Palestinian woman was shot while trying to stab an Israeli policeman in the flashpoint city of Hebron in the occupied West Bank.
Palestinians in the area attempted to approach the woman, who was left in critical condition, as Israeli border police tried to keep them back.
Some Palestinians then move forward toward the man in the wheelchair while another officer points his weapon at one of them, kicks him and orders him back, before firing a stun grenade.
The man was not seriously hurt in the scuffle.
One Palestinian online condemned "the savagery and cowardice of the occupation".
A spokeswoman for the Israeli justice ministry said "the case is under investigation" by its police investigations department, declining to provide further details.
Police spokesman Micky Rosenfeld said the incident occurred "a few minutes after a terrorist attack had taken place by a woman terrorist adjacent to that area".
"Border police dispersed the crowd and used non-lethal means. The man in the wheelchair was part of that crowd that had gathered."
Tensions have been high since a wave of Palestinian gun, knife and car-ramming attacks erupted at the start of October.
The violence has claimed the lives of 26 Israelis, as well as an American, a Sudanese and an Eritrean, according to an AFP count.
At the same time, 172 Palestinians have been killed, most while carrying out attacks but others during clashes and demonstrations.
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