Dusan Jovanovic from Belgrade's Emergency centre said the man, identified only by the initials D.H. by police, was admitted with "life-threatening" injuries.
"He was received with severe head injuries and bleeding, so he has undergone surgery and put in intensive care as his condition is very serious," Jovanovic told AFP.
The 26-year-old woke up later Saturday and communicated, but his condition "remains critical for next 24 hours," Health Minister Zlatibor Loncar told reporters after visiting the man.
Police said they had arrested all three perpetrators of the attack, which happened in downtown Belgrade, but gave no further details.
Earlier, Serbia's Interior Minister Nebojsa Stefanovic said he had ordered an urgent probe into the incident and vowed to find those responsible.
"We will not allow this kind of thing to remain unpunished... and we will arrest the German citizen's attackers," Stefanovic said in a statement.
The NGO Labris, which organised the conference on LGBT (lesbian, gay, bisexual and transsexual) rights, held a protest march along central Belgrade streets.
The incident occurred two weeks ahead of a scheduled gay pride parade, the first since more than 150 people were wounded in clashes between security forces and ultra-nationalists in 2010.
Authorities in deeply patriarchal Serbia have banned gay pride marches ever since, citing security reasons.