Darren Adie was refereeing a game between Newport County and Bath City Academy in the FA Youth Cup when the furore happened, The Sun reports.
In the first half, the referee ordered two Bath players, who were wearing white and black underwear respectively, to remove their offending items because the colours clashed with their red shorts.
Law 4 reads: "If undershorts are worn, they must be of the same main colour as the shorts."
With Bath temporarily down two men as the two players changed outside, Newport scored, igniting a number of confrontations which saw six members of the Bath team receiving a red card.
200 spectators eventually saw Newport win 6-0.
The Bath chairman said: "It was farcical. The players were made to strip in front of the crowd, which is quite an ordeal for lads aged 16 or 17."
The English Football Association is reported to be investigating the incident.
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