In a report on their website the club said some players missed training as they were giving police statements about the February 1 league game which also left up to 1,000 people injured after supporters of the Cairo club were set upon at the end of the match.
Training should have resumed last Friday but was postponed while players received counselling.
The club's football director Sayed Abdel-Hafiz said he was still trying to convince Barakat to change his mind.
"Barakat suffered a lot after the horrific disaster in Port Said. I still consider his decision as an emotional one that was taken in the heat of the moment," added Abdel-Hafiz.
"Ahly need Barakat who is not only a good player but also an icon. I will keep in touch with him and we will not give up hope to convince him to come out of retirement."
In statements submitted to the police, Jose and his players said Ahly's footballers were attacked and beaten as they fled the pitch following a mass invasion at the final whistle and then watched, cloistered in their changing room, as spectators died around them.
"Whether we play any ties at home in the competition will depend on the approval of security officials," said Ahly's director of football Sayed Abdelhafiz.
