The Yees and the senator's attorney, Jim Lassart, declined to comment outside court.
Other lawyers representing defendants in the case have argued that their clients were lured into the FBI sting by undercover agents who initially proposed much of the alleged wrongdoing.
Tony Serra, a lawyer for Raymond Chow, the leader of the Chinatown organization the FBI says is a front for organized crime, said "the government financed the crime."
"Law enforcement is supposed to investigate crime and criminal activity. In this case, they created crime and criminal activity," Serra said outside court. "This is political, and (Chow) is truly an innocent person."
Chow remained jailed on charges that include money laundering and receiving stolen property. He didn't enter a plea Tuesday.
Keith Jackson, the former San Francisco school board president who served as a political consultant to Yee and, separately, to Chow's organization, pleaded not guilty to corruption, conspiracy, firearms trafficking and murder-for-hire charges. He is free on $250,000 bond.
Some 29 suspects were indicted last week after 20 people, including Yee, Chow and Jackson, were arrested on March 26. Several others have been arrested outside California and will have to appear in court in San Francisco at some point.
Authorities say Jackson served as a middleman between Yee and the crime syndicate and helped funnel cash to the politician in exchange for political influence.
At the time Jackson was working for Yee, Jackson also was serving as a consultant to the Chinatown organization Ghee Kung Tong, the FBI claims. The tong portrays itself as a civic booster and community helper.
However, the FBI alleges it has served as a front for the headquarters of the crime syndicate led by Chow.
Yee, Jackson, Chow and most of the other defendants were ordered back to court on Friday for their first appearance before U.S. District Judge Charles Breyer, who will preside over the case through trial.