The 18-year-old Yorkshire batsman sat out England’s 32-run win over host nation New Zealand in Queenstown on Tuesday, with Will Jacks leading the side in his absence.
Coach Jon Lewis said after the match that Brook had been omitted for breaking a team rule, but did not give any details about what the breach was.
Lewis said: “Harry missed the match because he broke a team rule, so we decided to leave him out and deal with it internally. We’ll let you know if anything happens after that.”
Asked if it was a serious breach, Lewis added: “He just broke a team rule.”
Brook had been averaging 119.5 in the tournament with 239 runs in five innings, including one century and two half-centuries.
However, he could not prevent England from being knocked out by Australia in the Super League quarter-finals, with the win over New Zealand coming in the play-off for seventh place.
English cricket has been hit by several disciplinary issues in recent months, including Ben Stokes’ much-publicised arrest, but Lewis was keen to point out that the U19 team had been “extremely well behaved” in New Zealand.
He said: “The team exists and the rules apply to everyone so the captain breaks the rule and he missed the game.
“One thing I would like to stress about this group of people is that they’ve been extremely well behaved here in New Zealand.
“They’re a really good group of people. We take a lot of pride in our duty of care for the Under-19s as a support staff and we do put rules in place.
“If rules are broken then disciplinary action sometimes needs to be taken.”
He is not the only senior England player to have hit the headlines for negative reasons in the past few months.
All-rounder Ben Stokes missed the Ashes tour after being arrested following an incident outside a Bristol nightclub in September, and he will appear at Bristol Magistrates’ Court on a charge of affray on February 13.
The England and Wales Cricket Board fined and issued written warnings to Jonny Bairstow, Jake Ball and Liam Plunkett following an investigation into behaviour during the ODI series against the West Indies.
Bairstow found himself in the spotlight Down Under as well after greeting Cameron Bancroft with what the Australian opener described as a “headbutt” in a Perth bar on the first night of England’s tour in October.
Lions batsman Ben Duckett, meanwhile, was sanctioned by the ECB after pouring beer over Test star James Anderson, also in a Perth bar, in December.