Three of the eight member universities have now left the Hong Kong Federation of Students (HKFS), the student organisation that led the pro-democracy Occupy protests last year.
A ballot at the Polytechnic University last Wednesday drew 1,700 students, with 1,190 voting to quit the federation and 403 opting to stay.
A day later, Baptist University also cut ties with HKFS following a ballot where 1,678 students turned up to vote. A total of 914 students wanted out, while 613 wanted in.
Turnout rate was low in both universities; less than 10 per cent at PolyU and 15 per cent at Baptist University.
The University of Hong Kong's student union had already voted to leave the student body earlier this year.
HKFS has been criticised for making bad decisions during Occupy and missing chances to take stronger action against the government.
Secretary-general Nathan Law Kwun-chung said last week he is worried about the federation's future.
He admitted that with so many member universities leaving, the federation had been distracted from major issues, like the 2017 political reform package.
Before they can concentrate on fixing big social issues like that, they need to fix the problems within HKFS, he said.
"We really can't handle these things at the same time," he added.
Law's deputy, Wong Ka-fai, said that big plans, like last year's joint-university class boycotts that took place just before Occupy Central, would no longer be possible. "If more member institutions quit, we have to face the question: Is the federation still representative? What does it stand for?" added Law.
Five universities now remain in the federation, including City University. CityU will hold a ballot from tomorrow until May 6 to decide if they will also leave the federation.