Gatland has declared his full approval of the decision which was taken during discussions with WRU Group Chief Executive Roger Lewis about his prognosis for recuperation and recovery over the weeks ahead.
Lewis says the decision will offer certainty to players, coaches and supporters as the preparations and planning for the matches now enter an important preliminary phase.
The decision was taken after medical advice given to Gatland and his family in New Zealand was set against the huge scale and importance of the summer series of games in 2012.
Wales will play the Barbarians on June 2 (kick off 2pm) in a full international before the start of the biggest ever one-nation tour in the history of the Welsh Rugby Union outside a Rugby World Cup campaign.
Wales play an unprecedented three Test matches against Australia plus a midweek fixture against the Brumbies between the first and second Test.
Doctors have ruled out a return to Wales for Gatland in time for the Barbarians international and the latest medical advice is that he is unlikely to have recuperated sufficiently to take charge of Wales in Australia before the first Test match in Brisbane on June 9.
If Gatland recovers in time to join the squad for the final two June Test matches Howley will remain as caretaker with the Head Coach playing a supportive role.
Howley will continue to liaise directly with Warren Gatland throughout his current phase of recuperation, but the pair have agreed that the caretaker coach will make the final decisions required.
Roger Lewis said: "Our priorities are clear and we have acted decisively to ensure absolute clarity in the weeks ahead.
"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, Warren and I have talked this through thoroughly and it makes absolute sense to ensure the chain of command and authority levels are recognised.
"Warren can now concentrate on getting back to robust health before taking back full control of Wales to continue the great work he has already achieved and Rob can take this opportunity to develop as a coach at the highest level.
"The appointment of Rob Howley as caretaker coach is deeply significant for our long term succession planning. Rob has the total support of all of us at the WRU. This is an opportunity for us all in these unforeseen circumstances.
"We have an outstanding team of coaches and management all of whom are critically important to the success of the national team."
Gatland will not undergo immediate surgery as his injuries are given time to heal before any further decisions are taken on the need for intervention.
He was injured at home in a fall from the railings around decking at his Waihi beach house and suffered multiple fractures to the calcaneus or heel bone in his right foot and a fracture to the same bone in his left.
He has been advised that the injury to his right foot is severe and it is unlikely he would be able to bear weight on the limb by early June.
Howley said: "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.
"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."
Warren Gatland 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."
The Board of the WRU has decided unanimously that full caps will be awarded for the Wales team to play the Barbarians at the Millennium Stadium to kick off the summer action.
Some of the players not selected for the Barbarians game will fly to Australia before the Barbarians encounter to start their acclimatisation and preparation programme.
After the Baa Baas game the full squad will gather in Brisbane to take part in the training schedule from the Tuesday onwards.
As caretaker coach Howley will remain with the squad in Wales for the Barbarians international before heading out with them to Australia.
Howley, a former scrum-half who made 59 appearances for his country, won his first cap against the Barbarians in October 2001, in a game which also saw Wales' most capped forward Martyn Williams (99) and fellow flanker Kingsley Jones (10) make their respective debuts.
Wales have awarded caps for fixtures against the Barbarians on three previous occasions, the loss last November, the occasion of Williams' and Jones' debuts in 2001 and in the Baa-Baas centenary year of 1990.