A retired officer, aged 48, was also arrested on suspicion of perverting the course of justice. All three are being questioned at a London police station.
Rigg, who suffered from schizophrenia, died in August 2008 after being held in the prone position for more than eight minutes by officers on the Weir Estate.
An inquest last year uncovered a “litany of apalling failures” by police and mental health workers in the run up to Rigg’s death in a cell in Brixton police station.
An Independent Police Complaints Commission (IPCC) spokesman said: “IPCC investigators have carried out searches at their home addresses and the serving officers’ workplaces.
“Mr Rigg’s family have been told about today’s developments through their solicitors.”
Sean’s family, which continues to fight for justice, last year held an emotional vigil on the fourth anniversary of his death.