Shawkey has since declined requests for comment.
Neither Smith nor Roeder would comment about the situation, citing city personnel rules. Officials from the Orange County district attorney's office said they have not received any criminal complaints against Smith or Shawkey.
Smith, a former Officer of the Year in Costa Mesa, oversaw the investigation of a double-murder case earlier this year in which the victims were an Army veteran and an Orange Coast College student.
Smith maxed out his pension at 90% about two years ago but stayed on with the Police Department, even as the city offered incentives for veteran officers to retire because of budget restraints.
High-ranking police and city officials have said that Shawkey and Smith were frequently unavailable at department headquarters. Smith also teaches criminal justice classes at Golden West College in Huntington Beach.
Roeder would not say if absenteeism was involved in the decision to put the men on leave, or when and if they might be reactivated.
With Shawkey and Smith out, the department's top leadership has been cut by two-thirds. Capt. Les Gogerty is the acting chief, with lieutenants reporting below him. There are no other sworn captains in the department.
It was not immediately clear how Smith's retirement would affect the city's investigation.