The bodies of the four victims were found charred beyond recognition and it remains unclear whether any of them were children, the authorities said at a press conference, adding that also five survivors are yet to be identified.
Most of the passengers were Slovenian nationals, while two people on board were Italian and two were British, according to the police. Among those on board, six were children.
Ten victims required resuscitation, while the latest reports put the number of those who remain in critical condition at eight. The pilot and the co-pilot are among them, according to reports by commercial broadcaster POP TV.
The majority of survivors suffered various degrees of burns, many have fractured spines and lower limbs.
Speaking after completing preliminary surveying of the crash site, air-crash investigator Roman Rovanšek said that wind shear - sudden changes in speed and direction of wind - near the ground caused difficulty in controlling the balloon as the pilot attempted to land.
Accounts from survivors and eyewitnesses indicate that the balloon had trouble landing. It hit the ground hard and continued to move with horizontal speed before striking a tree and bursting into flames.
One of the passengers, Tomaž Šimnec, told the 24ur.com web portal that the balloon bounced off after hitting the ground too quickly. Some people were thrown out of the gondola and the balloon caught fire.
"I fell out of the gondola and lost consciousness, after which the gondola caught fire," Šimnec said.
There was another hot air balloon flying near the town of Ig about 10 km from Ljubljana at the time of the accident, but it managed a safe landing.
While the last weather forecast issued on Wednesday did not include storms for Thursday morning, they could have been detected on the charts about two hours before they reached the area, Brane Gregorčič from the Environment Agency (ARSO) explained.
"In fact one could see with the naked eye an hour before that clouds were gathering in the west," he added.
However, aviation meteorologist at ARSO Andrej Hribar said that the agency had issued the first warning for air traffic shortly before 7 AM.
Several other pilots have since said that they cancelled planned flights due to the weather conditions. One of these was Grega Trček from the local balloon club Balonarski center Barje, who said that "one does not fly in such weather".
The pilot of the other balloon that was in the air at the time, Rado Petrovič, however told the national broadcaster RTV Slovenia that he had checked the weather several times, including just before the flight and no storms were forecast.
What is more, the head of the Civil Aviation Agency Žiga Kotnik told the broadcaster that the pilot of the crashed balloon did not have a valid licence. It was revoked on 7 June after he failed to undergo a medical check-up required by the agency.
The site of the crash was visited by Defence Minister Alojz Hojs and Interior Minister Vinko Gorenak, who conveyed condolences to families of the victims. President Danilo Türk and PM Janez Janša also expressed sympathy.