"Thugs and hooligans who believe they can hold the organisation to ransom through their despicable behaviour will be dealt with in the harshest possible manner," said Malema on Monday.
"The code of conduct contained in the ANCYL constitution is unambiguous about the kind of conduct that is acceptable of a cadre of the Youth League, and this does not include exposing bare bums and hurling chairs at leadership and fellow delegates."
The Times newspaper ran a front page picture of a delegate pulling his pants down for the camera at the conference.
The events were also criticised by ANC deputy president Kgalema Motlanthe.
Malema said if the disruptions were in the name of campaigning for either himself or Saki Mofokeng the league should be embarrassed and distance themselves from the "uncomradely conduct".
He reiterated a previous apology for the incident, by outgoing president Fikile Mbalula.
Despite what was said in the media, much work was done, he said, but conceded that commissions to chart the way forward did not sit and the election of 30 additional members of the NEC were "placed in abeyance" pending the resolution of the complaints by a number of people.
Congress agreed to refer the matters to the ANC for guidance and leadership.
At a meeting last week the ANC reaffirmed Malema's leadership, clearing the electoral process, spokesman Zizi Kodwa said.
The league's congress would reconvene in June to conclude its business, which includes the election of the rest of the National Executive Committee.
Mofokeng could not immediately be reached for comment.
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