Israeli Police spokesman Micky Rosenfeld said on Monday the 60-year-old man was walking in an area of the Qalandiya Crossing north of Jerusalem al-Quds where only vehicles are permitted.
Rosenfeld said security guards ordered the man to stop but he continued to "approach them suspiciously", Al Jazeera reported.
They then shot him in the legs. Rosenfeld claimed it was only then that the guards discovered the man did not respond because he "cannot hear or communicate".
The incident comes less than three months after Israeli police shot and killed a 32-year-old Palestinian with severe autism.
The man was chased by Israeli border police forces into a nook in Jerusalem's Old City and fatally shot as he cowered next to a rubbish bin after apparently being mistaken for an attacker.
The shooting sparked great criticism and calls for police to amend their open-fire guidelines to take into consideration those with disabilities.
Palestinians and human rights groups have long accused Israeli security forces of using excessive force.
Heba Yazbak, a Palestinian citizen of Israel and Arab lawmaker, said Monday's incident exposed trigger-happy Israeli forces.
"First they shoot, and then they check," she said. "The shooting of an innocent deaf Palestinian is just another example of the ease in which Israeli security forces can harm human life."