Judy Kovco told ABC television she is convinced her son did not commit suicide or shoot himself accidentally while playing around with his gun.
Mrs Kovco said she was prepared for the possibility the inquiry would deliver an open finding, but she would fight for the truth as long as it took.
Asked whether she thought a major cover-up had taken place, Mrs Kovco told The 7.30 report: "I certainly do, yes, without doubt".
"They've done it in the past (been complicit in a cover-up)."
Ms Kovco said her son was too careful to have been fooling around with his gun and to shoot himself accidentally.
She said the inquiry had heard evidence that her son was not involved in an army culture of playing around with weapons.
"Everyone of those boys said Jacob did not join in those games."
However it was revealed yesterday that the inquiry may pin part of the blame on the Victorian soldier for his own death.
Lawyers warned
Lawyers representing some of the inquiry's key witnesses have been warned their clients face possible adverse findings.
And board president, Group Captain Warren Cook, confirmed Pte Kovco's own lawyer had been warned that unfavourable findings could be made against the dead soldier.
While details of the possible findings against Pte Kovco have not been revealed publicly by the board, it is believed they could relate to allegations that he failed to unload his 9mm pistol the day he was shot.
The inquiry has also heard that Pte Kovco was reprimanded on separate occasions by two of his superiors for dangerously mishandling his pistol while in Iraq.
One of Pte Kovco's roommates, Pte Ray Johnson, has also claimed that plenty of soldiers saw his friend joking around with his pistol like a gun-slinging cowboy.
Meanwhile Pte Kovco's widow Shelly is expected to deliver an emotional personal statement to the inquiry today.
The three-man board of inquiry yesterday began hearing closing arguments about evidence relating to Pte Kovco's death in his Baghdad barracks on April 21 this year.