Police originally said they opened fire on Monday during a car-ramming attack targeting officers in the Shuafat refugee camp in Israeli-annexed east Jerusalem.
One of the men in the car was killed and the driver was wounded, police said. There were no casualties among the officers.
Today, police spokeswoman Luba Samri said they were now investigating the driver of the car, Ali Nimr, 20, for manslaughter, involuntary manslaughter, driving without a licence, driving under the influence of alcohol and reckless endangerment.
An inquiry has also been opened by the Israeli justice ministry unit that probes police activity, Samri said.
Israel's Channel 10 television broadcast video of the incident that appeared to show shots being fired after the car was stopped, with Mustafa Nimr already on the ground either wounded or dead.
The two men were returning to the camp after buying pizzas, a witness told Channel 10 on condition of anonymity.
Haaretz newspaper reported that Mustafa Nimr's Jewish girlfriend and his brother were following them in a second vehicle.
Haaretz quoted witnesses as saying the car did not endanger police and they were racing at the time.
The border police who opened fire had been in the camp for a separate raid, authorities said. Police carry out such raids regularly in search of weapons or wanted suspects.
In June, Israeli troops killed a Palestinian teenager after apparently mistaking his group for stone-throwers as they returned from a swim, sparking outrage and debate about the security forces' use of firearms.
Israeli forces say most of the Palestinians killed were carrying out knife, gun or car-ramming attacks.
Others were shot dead during protests and clashes, while some were killed in Israeli air strikes in the Gaza Strip.
Israel has faced accusations of excessive force in certain cases for allegedly shooting dead Palestinian attackers after they appeared to be subdued and posed no further threat.
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