Gatland will be staying at home in New Zealand rather than travelling across the Tasman after fracturing both heels in an accident a week-and-a-half ago.
Grand-Slam winning boss Gatland fell from a ladder when cleaning windows at his beach house on Easter Monday and doctors have now stated that he is unlikely to have recovered sufficiently prior to the first of three Tests with the Wallabies in Brisbane on June 9.
The Welsh Rugby Union have therefore handed 1997 and 2001 Lions scrum-half Howley, who, like Gatland, was an assistant coach on the 2009 Lions tour of South Africa, the reigns on a temporary basis until the end of the summer.
"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," said WRU chief executive Roger Lewis.
"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."