Tear gas and petrol bombs were fired during a stand-off at Chinese University and roads were blocked across the city.
The annual fundraising event challenges teams of four to complete the MacLehose Trail within a 48-hour time limit.
Hong Kong protests: Education Bureau announces that parents should decide if children attend school on Wednesday
They stressed that all campuses must remain open and that students should only travel under safe conditions.
Anti-government demonstrations took place at various locations around the city and transportation was disrupted for the second day in a row.
Office workers in Central occupied streets at lunchtime as 10 colleges in the city remained closed.
Hong Kong protests: Student shot and man set on fire in one of the most violent days of anti-government unrest
Tear gas, petrol bombs, barricades and pepper spray are used across multiple districts as demonstrators create traffic mayhem in a bid to spark a general strike
Hong Kong protests: Student shot remains in critical condition after surgery as arguments rage over force used by police
The 21-year-old underwent an operation to remove his right kidney and part of his liver after being hit with a live round on Monday morning.
The pests are infected with parasites that ‘mind control’ them to leave their nests and burrow into the ground to await death
Hong Kong protests: Charity against sexual violence condemns police attempt to discredit alleged rape victim
Association Concerning Sexual Violence Against Women states alleged victim had not made her allegations public.
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