Chelsea accused a section of their support of "embarrassing" the club by not observing the silence in memory of the Hillsborough disaster ahead of their FA Cup semi-final at Wembley.
The Blues issued a statement condemning the behaviour of "a very small minority of fans" before their 5-1 win over Tottenham.
A statement on the club's official website read: "Chelsea Football Club is extremely disappointed that a very small minority of fans embarrassed the club today by not honouring the moment's silence before kick-off.
"Chelsea FC believes all moments of respect should be honoured and today we pay our full respects to all those that suffered as a result of the Hillsborough disaster 23 years ago."
A small number of Chelsea fans chanted during the silence, a mark of respect to the 96 Liverpool fans who died at Hillsborough during an FA Cup semi-final between the Reds and Nottingham Forest.
Other fans booed the disruptive group when the silence, also in memory of Livorno's Piermario Morosini, was over. Morosini died on Saturday after collapsing on the pitch during his side's game with Pescara.
Liverpool's last-four clash with Everton took place on Saturday to avoid be played on the anniversary of the disaster.
Chelsea's interim manager Roberto Di Matteo was disappointed with the fans' actions.
He said: "We are extremely disappointed that a minority, or just a few, decided to speak or sing during the minute's silence and not respect it. We are disappointed."
It is understood that Chelsea will work with Wembley and the Football Association to try to identify the fans responsible.