Frank Lampard's goal against his former side in the 2-0 win at Stamford Bridge on Sunday was met with missiles being thrown onto the pitch from the visiting supporters
Two fans have been detained on suspicion of racially aggravated public order offences while one more was charged with the theft of a seat and another is in custody for suspected affray.
The incident took place following Frank Lampard's opening strike for the Blues, as coins and other objects were thrown in the direction of Chelsea's players as they celebrated the goal.
The Football Association has said that it will liaise with the police and both clubs before taking the necessary action against either club or its supporters.
The Hammers have issued provisional banning club orders against the two fans charged with racially aggravated behaviour.
A spokesman for the east London side stressed the club have a "zero tolerance" approach to racist behaviour.
These latest arrests come in the middle of an ongoing investigation by the police over anti-Semitic chants made by West Ham supporters at White Hart Lane in their game against Tottenham last year.