The airport tweeted on Saturday evening (25 March) to warn of potential delays on Sunday (26 March) owing to a "technical issue" affecting self-service bag drop machines.
It reiterated the advice on Sunday: "If you are travelling from Gatwick today please be prepared for some delays at check-in due to a technical issue affecting our self-service bag drop machines.
"We are working with the supplier to rectify this as soon as possible. Please contact your airline with any queries."
Responding to a passenger, the airport added: "Passengers may experience delays due to technical issues with a system of a third party that operates the self check-in kiosks. We apologise for any delays caused."
In a statement issued to the BBC on Sunday morning, Gatwick said significant progress had been made towards solving the issue. "The airport operation is running well this morning and passengers should plan their journey as usual."
The BBC spoke to several passengers at the weekend, who claimed delays of anywhere between 60 and 90 minutes, with queues snaking out of the terminal.