Earlier, Gatwick said it was "running well" and had made significant progress rectifying a technical issue which caused delays on Saturday.
But Elaine MacDonald, travelling on Sunday, described "absolute chaos" after queuing for about 90 minutes.
Gatwick said it had seen "some queuing" but overall it was "running as usual".
In a statement issued on Sunday morning, the airport said it had been working with the supplier to rectify the technical issue and significant progress had been made to fix it.
A Gatwick spokeswoman said: "The airport operation is running well this morning and passengers should plan their journey as usual.
"For any queries please contact your airline. There may be some delays due to air traffic control strikes in France."
Earlier on Sunday, the airport had indicated in a tweet that the technical issue was ongoing and had warned that passengers could still experience delays.