"We have filed an appeal with the ICC against the ban," Pakistan Cricket Board director of operations Salim Altaf told AFP on Friday.
Ahmed became the first bowler Monday banned from bowling in international cricket after an assessment by the University of Western Australia confirmed he had been bowling with an illegal action.
The ICC announced the decision on Monday and Ahmed has 14 days to appeal.
Altaf said the Pakistan Cricket Board had material from biomechanic experts to support its case, adding that not all of Ahmed's deliveries were found to be illegal.
"We sent Ahmed to Australia for tests in October and a letter from bowling expert Daryl Foster, which we have received on Thursday, showed not all of his deliveries were beyond the allowed limits," Altaf said.
Under new ICC rules, a bowler is allowed 15 degrees to straighten his arm, the limit visible to the naked eye.
The ICC would now form a review group to hear Ahmed's appeal, Altaf said.
He was first reported and suspended earlier this year but returned to international cricket following remedial work on his action and a full bio-mechanical analysis that showed he had made necessary adjustments to his bowling style.
But the 29-year-old Ahmed was reported a second time, during the first Test against England in Multan in November. He was reported under revised ICC bowling regulations by on-field umpires Simon Taufel and Billy Bowden and TV umpire Asad Rauf.
Under the new ICC process, a bowler reported and assessed as bowling illegally for a second time within two years of the first period of suspension receives a mandatory one-year ban.
Ahmed said he hoped he won justice through his appeal.
"I hope to get justice because this whole episode has made me a depression patient," said Ahmed who considered quitting the game after the ICC ban.