Airlines operating from the Jomo Kenyatta International Airport (JKIA) in Nairobi were forced to divert to neighboring airports for fueling.
This emerged after stocks of the commodity neared depletion at JKIA as fuel shortage are expected to persist until Sunday.
The shortage was blamed on inadequate orders by oil marketing companies that sell directly to airlines.
JKIA at a standstill as workers go on strike
Fuel shortage
However, Kenya Civil Aviation Authority director-general Gilbert Kibe said a fresh delivery had arrived in Mombasa and was to be pumped to Nairobi to end the shortage.
The shortage comes in the wake of a strike by aviation workers who are protesting against alleged unfair staff hiring, poor remuneration and the proposed KQ takeover.
Aviation workers demanded the removal from office of KAA Chief Executive Johnny Andersen and chairman of the board Isaac Awuondo and their KQ counterparts.
Flights redirected
They have also opposed the planned takeover of JKIA operations by KQ, claiming their members will be rendered jobless.
GSU officers disperse striking aviation workers at JKIA
During the strike, flights to Amsterdam, Mumbai and London were delayed by more than six hours, taking off in the afternoon.
The government deployed Kenya Air Force personnel in an attempt to manage the damage, but most of the flights had already cancelled.