Kenya Air Force personnel were on Wednesday deployed to JKIA to handle the situation following a strike by aviation workers.
The military workers were positioned at the airport to help with the screening of passengers in a bid to help operations resume normalcy.
Addressing the media, Transport CS James Macharia assured that contingency plans were in place to ensure a quick resumption of activities at the airport.
"KAA in collaboration with KQ and with the support of Kenya Air Force managed to get a replacement of the screeners. As we speak we have the capacity to screen passengers departing and I can assure you that within the hour we shall have the first airplane flying out.
"I would like to commend the management teams of the Kenya Airports Authority and KQ, the relevant security agencies, for taking quick decisive action to ensure that normal operations resume as soon as possible," he stated.
All the morning flights to and from the airport were disrupted as the aviation workers began their strike with JKIA bound flights being diverted to other airports.
Sources indicated that the workers grounded all flights since 3am leaving thousands of passengers stranded.
Earlier in the morning, GSU officers were deployed to the airport to disperse the striking workers with KAWU Secretary-General Moses Ndiema being arrested during the protests.
Reports indicate that at least six airport workers, including flight attendants, sustained serious injuries as the police engaged them in running battles.
