The south London airport said it would be forced to cancel 164 flights while the limit is in place until October 1, in a bid to avoid even more cancellations and delays.
The airport said it would be limited to 800 flights per day until then, with the hardest-hit day set to be Friday.
It said this was caused by sickness among flight control staff.
The UK’s provider of air traffic control services, NATS, said 30 per cent of its staff were unavailable, with some having contracted Covid-19.
Stewart Wingate, CEO of London Gatwick, said: “This has been a difficult decision but the action we have taken today means our airlines can fly reliable flight programmes, which gives passengers more certainty that they will not face last minute cancellations.
“We are working closely with NATS to build resilience in the control tower, and this decision means we can prevent as much disruptions as possible.
“London Gatwick would like to apologise to any passengers who have been impacted by these restrictions.”
NATS said it is training additional air traffic controllers and expects another group to begin work in the tower at Gatwick “over coming months, ready for next summer”.
NATS said in a statement: “Even an experienced air traffic controller takes at least nine months to qualify at Gatwick and very few are able to do so, as Gatwick is such a busy and complex air traffic environment.”
Data from tracking website FlightRadar24 earlier Monday revealed that 64 flights to or from the West Sussex airport were axed across Sunday and Monday.
EasyJet made up dozens of the flights affected with some passengers facing delays of up to seven hours.
The airline said it was “extremely disappointed” by the issue which saw eight flights cancelled to and from Belfast. Other flights to or from Edinburgh, Geneva and Paris were also impacted.
An easyJet spokesperson said: “We are extremely disappointed that customers are once again being impacted by this and while this is outside of our control, we are sorry for the inconvenience caused to our customers.
“We are doing all possible to minimise the impact of the disruption and have notified those on cancelled flights of their options to rebook or receive a refund and are providing hotel accommodation and meals where required.”
It comes after the National Air Traffic Services control system was hit by a technical glitch in August.
More than a quarter of flights to and from UK airports were cancelled that day, affecting around 250,000 people.
Gatwick is expected to be affected by strikes this week after Aslef, the trade union representing train drivers, said it was taking industrial action.
The walkout will affect 16 train operating companies including Southern, owned by Govia Thameslink Railway, which runs the Gatwick Express – a service between London Victoria, Gatwick and Brighton. Aslef members will strike on Saturday and again on October 4.