Kenya's aviation workers have called off a strike that disrupted flights at its main international and other airports, Transport Minister Davis Chirchir and aviation workers union head Moss Ndiema said on Tuesday.

The strike, mostly by air traffic controllers on Sunday and Monday, disrupted several flights into and out of the main Jomo Kenyatta International Airport and delays spilt over to regional airports in East Africa and beyond, affecting thousands of travellers.

"We are simply calling off our strike action and pleading with our members to begin the process of normalising operations, restoring services," Ndiema told a press conference.

"For those who are on duty, we are asking them to begin clearing flights."

The Kenya Aviation Workers Union (KAWU) said its members went on strike over a longstanding failure of the Kenya Airports Authority (KAA) to finalise a new collective bargaining agreement.

It also opposed the use of volunteers from the National Youth Service as airport staff.