Gatland, 48, is recovering in New Zealand from a recent fall when he fractured both heels.
He will also miss the summer international against the Barbarians.
"Although I am devastated to be away from the action I am delighted that we have someone of Rob's calibre to take charge in my absence," said Gatland.
"I know Rob will be his own man as caretaker coach, but he and I share a similar vision about the international game so the players and coaches will know what is expected of them."
Howley, a former scrum-half who made 59 appearances for Wales, said he is "proud" to be leading his country.
"We will be working to secure victory against the Barbarians after the defeat we suffered last year and the Tests in Australia are an opportunity for us to deliver a win in the southern hemisphere," he said.
"Along with the rest of the coaching team I am immensely proud to have been offered this opportunity and we will give our all until Warren is ready to take full control again."
Gatland, who guided Wales to a second Grand Slam of his reign this season, is likely to coach the 2013 British and Irish Lions' tour to Australia.
He will not undergo immediate surgery but has been advised that the injury to his right foot is severe and that he is unlikely to be able to bear weight on it by early June.
"Our priorities are clear and we have acted decisively to ensure absolute clarity in the weeks ahead," said WRU chief executive Roger Lewis.
"Warren has taken the appropriate medical advice and agrees that appointing Rob as caretaker coach in his absence is the best way forward for our Grand Slam winning squad.
"Rob has the total support of all of us at the WRU. This is an opportunity for us all in these unforeseen circumstances."
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