80-year-old Kalam was frisked in New York on September 29 before boarding an Air India flight.
Sources said that even after Kalam had taken his seat in the aircraft, the US security personnel forced the crew to open the door and took away the jacket and boots of the former president to check for explosives since they had forgotten to do so before his boarding. The items were later returned to Kalam.
Taking serious note of the incident, External Affairs Minister S M Krishna spoke to Indian Ambassador to US Nirupama Rao and directed her to take up the matter in writing at the "highest level" with Washington.
Officials said the Minister has also sought a detailed report on the incident from its mission into the incident which they said was "unacceptable".
They further said that if this continues, there is a possibility of reciprocating as per diplomatic norms.
Sources close to Kalam said he doesn't give much thought to such incidents and never complains about them.
However, this time, his office informed the Ministry of External Affairs about the incident after he returned home.
This is not the first time that Kalam has been frisked by US aviation officials.
Kalam was frisked by officials of US airliner Continental Airlines in April, 2009 despite his name featuring in the Bureau of Civil Aviation Security's list of people exempt from security checks in India.
A detailed report on the latest incident was prepared by Air India's Director (Security) S Mathur and sent to the Civil Aviation Ministry which in turn forwarded it to the External Affairs Ministry in October.
"As the incident happened on the American soil, I have been informed that US security agencies are investigating it now. Such incidents should not happen," Civil Aviation Secretary Nasim Zaidi told PTI.
An External Affairs Ministry spokesperson said officials of both the countries were working on ways to avoid recurrence of such incidents in future, including preparing a common list of VIPs.