Operations at the Jomo Kenyatta International airport have resumed after hours of delays after workers downed their tools.
More than 100 flights were canceled or rescheduled affecting thousands of passengers.
The impasse ended after the airport enlisted the help of Kenya Air-force personnel to control the air traffic.
Transport Cabinet Secretary James Macharia said the striking workers now stand to lose their jobs for disobeying court orders and engaging in an illegal strike.
At any given day Jomo Kenyatta international airport handles an average of 20 thousand passengers flying and landing from various destinations.
Hundreds of flights were grounded as Kenya Aviation Workers Union (KAWU) members went on a strike demanding improved working conditions and stop to the planned merger between the national carrier Kenya Airways and Jomo Kenyatta international airport.
Transport CS James Macharia said the striking workers now face the sack for jeopardizing the security of the aviation industry in the country.
Thousands of passengers were forced at camp at the hub for hours before Kenya Airforce personnel came to restore order at the facility.
The first flight left the airport at around 12 headed to London almost 8 hours late.
The Kenya Private Sector Alliance (KEPSA) urged all stakeholders to resolve the impasse quickly to allow normal operations to resume at JKIA.
Union officials and the striking workers were dispersed by security officers.
Earlier, Labour Relations Cs Ukur Yattani had called on the striking aviation workers to resume duty as ordered by the court.
Yattani said his Ministry had set up a conciliation committee chaired by Sharif Adbulkadir Sharif to help resolve issues raised by aviation workers who went on strike Wednesday morning paralyzing air transport operations countrywide.
The Sharif-led committee is expected to resolve grievances raised by parties and file a report within the next 30 days.
Meanwhile, The Kenya Association of Travel Agents (KATA) has called for the speedy resolution of the impasse between Kenyan Aviation industry players and the workers union to ensure normalcy returns at the JKIA.
“We would like to ask both parties to be conscious of the damage a prolonged strike could cause to the country’s aviation sector and urge them to amicably resolve their differences without resorting to unorthodox means,” said KATA through twitter its handle.
KATA urged travelers to ensure that they are in constant communication with their travel agents to receive updated information regarding the status of their flights.