The boys' bodies were found several hours apart after rescue crews and dogs resumed their search of the debris following a lengthy break forced by fears that the wrecked structure could further collapse. Eight children were among those confirmed dead.
Authorities said the boys and the missing girl were between 12 and 16, but did not give their individual ages. A 40-year-old woman was also missing as hopes faded of finding survivors after a second night of snow and freezing temperatures.
"There have been no signs of life," said police official Hubertus Andrae.
The roof caved in after heavy snowfall Monday afternoon with about 50 people inside, including many children on Christmas break from school.
Rudolf Schaupp, the deputy administrator of the district of Berchtesgaden, said relatives of the victims had been brought to the site. "Maybe it can't calm them but at least they know what the rescue crews are doing," he said.
On Tuesday afternoon, rescue efforts were halted after one of the collapsed ceiling crossbeams shifted.
Special cranes were brought in, and workers spent the night tearing away pieces of the facade and the remains of the roof. The rescue crews were able to enter the building a little before 4 a.m.
Fire official Rudi Zeif pledged Tuesday that "we will continue the search until we have rescued or recovered all the missing."
Asked if they could still be alive, he said earthquake victims had survived for several days.
Pumping warm air into the area was considered, but ruled out because it could melt snow, leaving any survivors wet and colder than before. Rescuers hoped the snow could produce an "igloo effect" that might create relatively warm pockets of air.
Rescuers using dogs, shovels and their hands found a 5-year-old girl with only minor injuries late Monday, but had found no one alive and heard no calls for help since then.
Several hundred people gathered Tuesday for a candlelight vigil at town hall, and church bells pealed for 20 minutes.
Prosecutors opened an investigation for possible negligence, an automatic step after a fatal accident.
All the victims came from the area around Bad Reichenhall, an Alpine spa town of 15,000 inhabitants on the Austrian border. People in the town questioned why a public building could not withstand a heavy but predictable snowfall.
"There's something rotten about this. We've had a lot more snow than this before," retiree Erna Schweiger-Nolte said as she stood outside the police cordon. "The politicians say, 'save, save, save,' but it shouldn't be on the wrong things."
She said it was known that the building, erected in 1972, was in poor shape and leaking.
Experts suggested a structural flaw was a more likely cause than the heavy snow that fell Monday.
An official with the town's ice hockey club said local authorities told him 30 minutes before the accident that a regular practice session for youth players later in the day was canceled because there was a risk of collapse.
Local officials said there was an 8-inch layer of snow on the roof at the time of the collapse. Mayor Wolfgang Heitmeier said that was well within the building's safety margin.
Still, town officials had planned to close the rink after the end of the day because the snow was continuing.