In the first version, episode 339, Kakashi was twelve and had become a jonin. Minato's team carried out the Kannabi Bridge mission, and during the mission, Minato said Hatake Sakumo had died five years earlier. By this version, Kakashi lost his father at seven.
These episodes were Kakashi Gaiden, which was also in the manga, serialized between Part One and Part Two.
The second version was the Book of Combat.
In the Book of Combat's setting, Kakashi was twenty-seven, and it mentioned that the Battle of Kannabi Bridge had taken place thirteen years earlier. By this version, Kakashi was fourteen at the time, and five years before that meant he was nine.
In this version, Kakashi lost his father at nine.
The third version was episode 636.
Obito had not yet graduated when he heard passersby say Kakashi was difficult to get along with. Only then did he recall that Kakashi's personality had changed drastically since their last meeting.
The Third Hokage assigned Minato to be Kakashi's instructor and mentioned Hatake Sakumo's death. Not long afterward, Obito graduated and joined Minato's team.
This episode was anime-original.
Of the three versions I knew, none said Kakashi lost his father before graduating. Sakumo died when Kakashi was roughly seven to nine years old.