Chaney was identified as the supervisor who was allowed to retire, while Stokes was "removed with cause" and can appeal the decision within 30 days, CBS said.
A third agent resigned and at least eight other Secret Service personnel and 10 military personnel are being investigated, the broadcaster said.
Mark Sullivan, director of the Secret Service, told lawmakers Wednesday one of the three agents removed from their posts plans to sue, CBS reported. The remaining eight are on leave with suspended security clearances, and the military service members were returned to their home bases.
Agents have provided differing accounts of events in Cartagena, Colombia, that led up to a prostitution scandal, lawmakers and others said.
They have "different recollections about what happened, or are not telling the truth," House Homeland Security Committee Chairman Peter King, R-N.Y., said.
King Thursday told the Los Angeles Times more resignations may be imminent.
"It is our understanding the resignations could come today or tomorrow," King said after speaking with Sullivan.
Some of the men said they were unmarried and brought to their hotel rooms women they met at bars, and said they did not pay for sex, a person familiar with the case told The Wall Street Journal.
Others said they visited a nightspot widely known as a brothel, and still others said they went to a club where they met women they didn't think were prostitutes, the person told the newspaper.
The varying versions of the April 11 events -- which unfolded as the agents and officers visited nightspots in the Caribbean port city two days before the start of the Summit of the Americas gathering of regional presidents -- came as the Secret Service announced the departure of two agency supervisors and another employee linked to the scandal.
U.S. Sen. Mary Landrieu, D-La., chairman of the Senate Appropriations subcommittee on homeland security, called the men's alleged misbehavior a "gross violation of public trust."
Presumptive Republican presidential nominee Mitt Romney said Wednesday he would "clean house" at the agency.
He later said he had faith in Sullivan's leadership. Sullivan was appointed to his post by President George W. Bush in 2006.