People attending the festival on Anglesey on Monday were asked to take shuttle buses to the Bodedern Maes from the Anglesey Show ground at Mona.
But some visitors complained of waiting up to two hours for a bus.
Eisteddfod chief executive Elfed Roberts had urged visitors to "be patient".
He said the change was a "temporary measure" to conserve the ground.
"The rain yesterday was horrendous, that's what was at fault," Mr Roberts added.
"There are people complaining that there is some mud on the Maes, I don't think that any field anywhere would have coped with what we got last night.
"We all need to be patient, we need to calm down and not panic."
The shuttle bus system will stay in place on Tuesday.
Blue badge holders should park in Ysgol Uwchradd Bodedern, with a system in place to bring people to and from the Maes.
Organisers of the National Eisteddfod have apologised for delays following a decision to shut the main car park after it became waterlogged.