Police were called to the club's training ground following a clash between the players as they prepared for Sunday's Premier League game with Tottenham.
The Daily Mail reports that the mother of a youth-team player made the call after witnessing Flores brandishing a brick.
However, while the club confirmed that a clash between the two had taken place, they dismissed suggestions that any threats had been made, adding that no action had been taken.
"Chico Flores and Garry Monk had an exchange of words, which is not uncommon between players in training grounds across the country, but no threats or altercations took place between the players in question," said a club spokesman.
"It's understood a member of the public phoned the police, who felt no action was required.
"The matter has been dealt with and is concluded."
A statement from South Wales Police said: "Police were called to the training ground at around 130pm on Friday 17 January. Club officials were spoken to and no police action was required.
Former captain Monk has not played since September after suffering a knee injury, while Flores, who joined from Genoa in the summer of 2012, has been a regular in the side, making 29 appearances.