"The decision was taken after Egyptian FA president Samir Zaher discussed the matter with coach Hassan Shehata and team doctor Ahmed Maged," Shalabi revealed.
"Zidan previously said he wouldn't be able to take part in the World Cup qualifier against DR Congo on Sunday because of stomach injury.
"However, medical tests showed that his injury is a slight one and that it shouldn't hinder his participation with the national team."
Shalabi said the Hamburg forward will be ruled out of Egypt's first four qualifiers, which will be played on successive weekends in June.
"Zidan explained that he wanted to get some rest before beginning his pre-season preparations with Hamburg," he added.
The former Mainz man is the third player to pull out of Egypt's squad.
Ahli playmaker Mohamed Abou-Treika and Middlesbrough's Mohamed Shawky have been already ruled out of the four qualifiers due to injury.