Sir Bernard Hogan-Howe told the Victoria Derbyshire Show he was "worried" police officers were put "in the same position as the criminal".
He said officers should not be criminalised over job requirements.
A former Met firearms officer who shot dead Azelle Rodney was recently cleared of murder 10 years after the shooting.
Mr Rodney, 24, was shot six times after firearms officer Anthony Long believed his colleagues were in "imminent" danger during a police operation to foil an attempted robbery in Mill Hill, north London, in April 2005.
Sir Bernard said he was "really concerned" about the case but had expressed his "regret" for what had happened and offered to meet Mr Rodney's mother now the case was over.
He said: "I am worried that in law we're putting officers in a position that is the same as the criminal who decided to go out with a firearm, decided to commit a crime.
"They made that choice, and then the officer takes the right action and it still seems as though they're having to explain it 10 years later.
"That worries me and I think in law we've got to look at it."
Sir Bernard said he understood the reasons why a prosecution was eventually brought in the case of Mr Rodney and said his death was a "terrible" thing for his mother, Susan Alexander.
But Sir Bernard criticised the "very forensic analysis" that takes place after a police decision to open fire.
"The officers who come forward to carry firearms are volunteers on behalf of society, the 60 million of us, they're the ones we ask to go and confront criminals who have, or we believe they have, firearms," he said.
"I really worry on behalf of our officers in that split second they have to make a decision, not only are they thinking about the present circumstances, are they thinking more about what might come next - and they may therefore make the wrong decision?"
He added: "I think sometimes the people who judge them later haven't had that experience. They don't understand that momentary judgment which is really quite a difficult one."
Sir Bernard's five-year term as Met Commissioner ends in September 2016.  Asked whether he'd like to stay on for "another couple of years", he said he'd "like to" because he loved the job and there was a lot still to do.
The Met's Commissioner has called for a review of the law around the prosecution of firearms officers involved in police shootings.