Gatland is still recuperating in his native New Zealand after fracturing both his heels in a fall at his beachhouse.
It was originally hoped he would recover sufficiently to lead Wales Down Under but with doctors ruling he will not be able to put weight on his right foot, it was decided Howley - normally attack coach - will take charge.
But Gatland maintains he has no qualms about handing the reins to the former Wales scrum-half.
He said: "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.
"I have talked through all the potential scenarios with Rob Howley and Roger Lewis, but the medical advice is clear and cannot be ignored.
"I will not be ready to take charge of Wales for the international against the Barbarians and if I recover enough to get to Australia during June I am still unlikely to be mobile enough to play a full coaching role.
"It has been difficult to accept that advice, but it just makes me more determined than ever to get back into the driving seat with Wales later on this summer as we prepare for an Autumn series which includes games against New Zealand and Australia.
"During my time in Wales we've put in some young coaches who have developed significantly over the past few years and I believe they are capable of stepping up to the job.
"As coaches we debate selections and strategies vigorously and we don't always agree, but once a decision is made we all support it totally. I know the Welsh people won't always agree with some of those selection decisions and they have a right to their views, but I would ask them to offer the same kind of support to the coaches once those decisions have been made.
"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."
Together with defence coach Shaun Edwards, kicking coach Neil Jenkins and forwards coach Robin McBryde, Gatland and Howley have masterminded two RBS 6 Nations Grand Slams in the last four years.
But Wales' record against Southern Hemisphere opposition is poor after losing to both South Africa and Australia in the 2011 World Cup, and Howley is aware of the pressure for the Six Nations champions to prove their worth on the world stage.
"I will give one hundred per cent of my effort to ensuring we are fully prepared to meet the challenges and take the great opportunities which lie ahead in this summer series," he said.
"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.
"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.
"The players know all about the roles and responsibilities we perform and what we all have to deliver for the national cause over the months ahead."