But Howley, who stepped in for the injured Warren Gatland on the tour, is confident that Priestland will rediscover the form that helped Wales to a Grand Slam in the RBS 6 Nations earlier this year.
He told walesonline: "Rhys has played a huge part in what Wales have achieved over the last 12 months.
"Everyone knows about his performances at the World Cup and he was exceptional in the second half of the Grand Slam game against France in terms of playing territory.
"Rhys knows in certain components of his game he wasn't at his best in Australia and that overall his play wasn't to the standard he achieved in the World Cup.
"But he has only been playing at ten for Wales for ten months
"You talk to Neil Jenkins about the criticism he had over a decade of playing there.
"Number ten has always been a big focus in Wales and that will never change.
"Our overriding opinion throughout the Test series was that Rhys was our number one fly-half. And I still believe that to be the case.
"There are always going to be challenges for Rhys moving forward in his game.
"It will be interesting to watch the couple of months in September, October going into the autumn series.
"But, to my mind, he is still our number one fly-half."