Mayor Tom Bates said investigators believe the wood was not caulked and sealed properly at the time of construction and was damaged by moisture as a result.
The crowded fifth-floor balcony broke off an apartment building during a 21st-birthday party early Tuesday held by visiting Irish college students, dumping 13 people 50 feet onto the pavement. In addition to the six killed, seven were seriously hurt.
"More than likely it was caused by rain and caused by water damage that was done to the support beams," Bates said. He said it was "obviously a bad idea" for 13 people to crowd onto such a small balcony - it was about 40 square feet - but added that he is not blaming the victims.
Later in the day, however, the mayor said the water-damage theory was speculation on his part and not an official conclusion, and that the investigation is still underway.
Building inspectors also determined another balcony at the Library Gardens apartment complex was "structurally unsafe and presented a collapse hazard." They ordered it demolished.
Two other balconies were red-tagged, or declared off-limits, at the apartments, which were completed in 2007 and are popular among visiting students and those at the nearby University of California, Berkeley.
Segue Construction, the Library Gardens general contractor, was involved in two San Francisco Bay Area lawsuits in recent years involving allegations of dry rot and substandard balconies at condo and apartment projects in Millbrae and San Jose. Among other things, Segue was accused of improperly waterproofing balconies.
Both cases were settled in 2013 with Segue, developers and other parties agreeing to pay millions of dollars.
Segue spokesman Sam Singer said such litigation is common on large projects and "has no bearing on the tragedy" in Berkeley.
"They are completely different projects. They are completely different types of balconies," he said. Singer said of the balcony collapse: "Segue Construction has never had an incident like this in its history."
Cassandra Bujarski, a spokeswoman for the apartments' property management firm, Greystar, had no comment.
Across the Atlantic, flags flew at half-staff around Ireland and the country's parliament suspended normal business as the nation mourned the dead: Ashley Donohoe, 22, of Rohnert Park, California, and Olivia Burke, Eoghan Culligan, Niccolai Schuster, Lorcan Miller and Eimear Walsh, all 21-year-olds from Ireland.
"They were in the prime of their lives," said Bernadette Prendiville, principal of the high school from which Burke and Walsh graduated. "They had a successful time in school, went about their work quietly and had everything going for them, everything ahead of them."
Josh Wilson, assistant principal at Rancho Cotate High School, said Donohoe was a remarkably well-liked and cheerful young woman who returned after graduating to help coach the soccer team.
"She just always had a smile on her face and transcended peer groups and cliques and had a friend in just about every social circle," he said.
PHOTOS: Several killed in balcony collapse in Berkeley
Grieving family members declined to speak with the media after arriving from Ireland and being met at San Francisco International Airport by a priest and representatives from the Irish Consulate.
Later Wednesday night a Mass was held at a cathedral in nearby Oakland in the students honor. The gathering of about 300 people, which included some fellow Irish students but no relatives of the victims, heard "Amazing Grace" played on bagpipes as they mourned.
"All we can do is to pray, to love and to care for them," Father Aidan McAleenan, who had met with some of the victims, said at the Mass.
The Irish students were working and traveling in the U.S. over the summer, a rite of passage enjoyed by thousands of their countrymen.
"For many of my countrymen, this is a favorite experience, and to have this happen at the start of the season has left us frozen in shock," said Philip Grant, Ireland's San Francisco-based consul general.
McAleenan, who visited two of the injured at John Muir Medical Center in Walnut Creek, said they were doing fine, but friends of the dead and injured were in shock and having a hard time talking.
Darrick Hom, president of the Structural Engineers Association of Northern California, visited the site of the collapse and said he noticed the broken wooden beams under the balcony were crumbling in the hands of investigating engineers.
"That wood was decayed or had some serious deterioration to the point where they could touch it with their hands and it was coming off in chunks in their hands," Hom said. He said it was surprising to see such deterioration in a building just 8 years old.
Normally, any building material - wood, steel or concrete - that will be exposed to the elements requires weatherproofing at the time of construction, Hom said.
Nothing in state code requires follow-up inspections of balconies after a building is issued a certificate of occupancy, unless there is major remodeling, said Brian Ferguson, deputy director of the state Department of General Services.
Although Florida has some balcony inspection requirements, most places don't require any reviews after construction is complete. Lawrence Ubell, president of New York-based Accurate Building Inspectors, said that could spell trouble.
"Annual inspections are so important for all balconies and terraces, but particularly for ones made of wood," he said. "In fact, rotting wood is the biggest cause of balcony and terrace failures."
Sari Kosdon, a Berkeley graduate student who has lived at Library Gardens since last August, said she feels terrible about the Irish students' deaths.
"I see these kids all the time and they are just so happy to have gone to this country and the opportunity," she said. "I feel like as a country we've failed them."