Zidan was fined by the FA before being ruled out until further notice by coach Hassan Shehata for failing to show up on time of a friendly with Guinea.
The Borussia Dortmund striker also didn’t answer phone calls from the Egypt technical staff, who only received a late message from the German club saying that 'Zidan is injured'.
"Zidan is a very important player and we didn't want to do what we did, but he didn’t respect the national team," Zaher told Egyptian TV.
"We need our players focused in the following period, we should not succumb to the problems of one player."
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Zaher indicated that Zidan's international experience added to his value in Europe.
"We know he played in Europe since a long time, but he always has to remember that being part of the national team helped him brighten his name in Germany," he added.
"Zidan's presence with the Egypt squad in CAN 2008 changed his image in Europe."
Zidan played a role helping Egypt win their sixth African Cup of Nations title in Ghana last year, scoring a memorable double against Cameroon in the opener.
Meanwhile, Dortmund will host Spanish giants Real Madrid in a friendly on Wednesday night as the Bundesliga club celebrate their centennial.