Lee signed a law that makes clear, San Francisco police cannot ride roughshod over city and state privacy laws, even when it comes to counterterrorism.
"We wanted to make sure that we would not end up in the days of apology. That should be long gone," said Lee.
The FBI and San Francisco police made a secret agreement in 2007, outlining how they would work together on the Joint Terrorism Task Force. It authorized intelligence gathering not allowed under state law, like surveillance without any grounds of criminal suspicion.
The new law requires any new agreement have an open airing at the Police Commission and that police follow local privacy and first amendment standards.
"It says that to the extent the FBI are using our local police as a force multiplier, they can't impose their standards on our local folks," said Hyeong-Ju Rho with the Asian Law Caucus.
"They have to get approval, it can't be done in secret," said Mokhtar Alkhanshali from San Francisco.
Alkhanshali expects this law to protect basic freedoms he felt were threatened before.
"Both sides of my family were contacted by the FBI and our mosque was constantly under surveillance, and our businesses were constantly under surveillance," said Alkhanshali.
Supporters say the new law protects national security by assuring minority communities they're not being investigated based only on the way they look or the sound of their name.
"It opens the door for communities to actually reach out to police and say, 'This is what we're seeing in our community,' so it takes away the fear element of engaging with police," said Rho.
Police Chief Greg Suhr says he supports this version of the law.
"I think it's always important to have the conversation, but that I think we have to do what is reasonable and practical within the city's rules and department policies to keep the city safest," said Suhr.
Suhr says there's no way to know when or if a new FBI agreement will go before the commission.