Cardoso has sat on the bench of the Bundesliga side for their last two matches following the sacking of Michael Oenning, but under league rules, he is not permitted to work for more than a fortnight since he does not hold a suitable coaching licence.
The DFB yesterday confirmed that no exception would be made for Cardoso, but his club are to contest their decision.
"We are going to lodge an appeal," said the club's chairman Carl-Edgar Jarchow to Germany's dpa agency.
Since the club's search for a successor to Oenning has not yet delivered a solution, Hamburg would like to extend Cardoso's temporary spell in charge.
The uncertainty is not worrying the Argentinian, though.
"It is all out of my hands," he said on his club's website.
"I am enjoying working with the team and we have taken a step forwards in these two games, so that is good.
"Other people will now decide how things proceed. I just carry on working whether it is with the first or the second team.
"As long as the club need me, I will be there."
An alternative solution, should Hamburg's appeal be rejected and no new coach be found in the meantime, would be for the club's director of sport Frank Arnesen to take over as the official coach since he holds the required licence.
Assistant coach Frank Heinemann and goalkeeper coach Ronny Teuber would also be eligible to act as head coach, although Cardoso is officially unable to sit on the bench in such a position for their clash with Freiburg on October 16.