A senior official of the board confirmed that the finance department had deducted the fine amount from the dues that were to be paid to Afridi for the World Cup and tour to West Indies.
"In total the board had to pay him around Rs. 5.5 million out of which we deducted the fine amount in full," the official said.
The disciplinary committee of the board had fined Afridi for several breaches of the code of conduct last month.
The fine came after a stand off between Afridi and the PCB allowing his removal as captain of the national one-day squad in May. He announced his retirement in protest and criticised the board for its conduct and not respecting senior players.
After he withdraw a case against the PCB from the Sindh High Court, Afridi appeared before the disciplinary committee which fined him but asked the board to issue him an NOC to go and play for Hampshire in England`s domestic Twenty20 event.
This is the second highest fine amount recovered from a Pakistani player by the board after the record Rs. seven million that were deducted from retired fast bowler Shoaib Akhtar`s dues.
The board official said the finance department had also deducted the half a million rupees fine from wicketkeeper Zulqarnain Haider who was also penalised by the disciplinary committee.
National selector, Mohammad Illyas who had a war of words with Afridi during the stand off with the board, also called up the all-rounder to inquire about his father`s health.
"Whatever happened is past now but at this time Afridi needs all our prayers and support so that his father can recover soon," Illyas said.