The names of Spurs defender Caulker, 20, and Leeds centre-back Lees, 21, have emerged in reports after it was confirmed Serbian police had submitted charges following last month's stormy England Under-21 international in Krusevac.
Coach Steve Wigley is also believed to have been charged.
The British government established, after contacting their counterparts in the Balkan country, that two players and one coach from England were facing charges relating to the Euro 2013 qualifier that ended in chaotic and violent scenes.
None of the three have been officially named as the Serbian public prosecutor determines whether to pursue the matter. The British Government, Football Association and the clubs will await developments before deciding how to proceed.
A statement from Spurs read: "The club has been in contact with the Football Association amid reports that our defender Steven Caulker has been charged by Serbian police in relation to alleged incidents that occurred during the recent England Under-21 international in Krusevac.
"At this time, neither the FA, the player nor the club have received any formal notification of a charge.
"The FA has confirmed that they will seek to determine the validity of such reports and the formal position and that they are continuing their discussions with the Government to bring this matter to a swift and satisfactory conclusion."
Leeds issued a similarly-worded statement concerning Lees, who appeared as a second-half substitute in the match in question, which was also marred by allegations of racist chanting.
The FA's position has not changed from Tuesday, when reports of the charges first emerged.
A statement from the governing body read: "The FA continues to remain in close contact with the UK Government regarding the continued media reports of Serbian Police charging England Under-21 players and staff.
"There remains no formal communication of any charges to The FA or the Government. However, we understand there has been a verbal communication of the names of the individuals concerned, which we now believe to be England players Steven Caulker and Tom Lees, and coach Steve Wigley.
"The FA would like to reaffirm its support for all of our players and staff and we have spoken with the players’ clubs and those named to express this.
"The FA has been taking legal advice in both the UK and Serbia to provide appropriate protection should any charges be brought.
"We welcome the support we are receiving from the UK Government."
Trouble flared after Connor Wickham struck in injury time for England to secure a 1-0 win and passage to next summer's finals in Israel courtesy of a 2-0 aggregate success. Missiles were thrown onto the pitch as players celebrated and the scenes turned uglier as some fans got onto the playing surface and there were clashes involving team members and staff of both teams.