Najam Sethi has taken over interim replacement.
The Pakistan Cricket Board said a scan on Monday had confirmed there was no signs of injury and Afridi's discomfort was likely 'due to a forced knee flexion'.
The Pakistan Cricket Board requested the Asian Cricket Council to convene an emergency meeting.
The BCCI, after its Annual General Meeting on Tuesday, concluded that it will not send its team to Pakistan for the Asia Cup.
Afridi has been sidelined since sustaining a ligament injury to his right knee during a Test match in Sri Lanka in July and missed the Asia Cup as well as the home series against England.
Hayden, 50, worked with the Babar Azam-led team as batting consultant when it reached the semifinals of last year's T20 World Cup in the United Arab Emirates.
Pacer Mohammad Wasim was sent for an MRI scan to determine the severity of his injury after he complained of lower back pain during a net session.
After Imran's ouster in April, there are reports that the new government is mulling to bring new leadership to the PCB.
The PCB said that Hasnain's bowling action has been found to be legal as the amount of elbow extension in the reassessment was within the 15-degree level of tolerance permitted under the ICC Illegal Bowling Regulations.
The Commonwealth Games Federation drew flak after media reports said Maroof's daughter had been denied accreditation, which would require the Pakistan batter to stay outside the Games village during the tournament.