The Saracens winger has already been ruled out of Saturday’s European Champions Cup final against Clermont Auvergne at Murrayfield and faces a race against time to be fit for the three-Test tour.
Maitland has damaged ankle ligaments and Saracens rugby director Mark McCall fears the player may need an operation.
“Sean is unfortunately out for the rest of the season, he’s got an ankle ligament injury,” said McCall.
“It may or may not need surgery, but we won’t find out for a few days.
“It’s cruel luck for a player who has been in such great form.
“I just feel sorry for Sean as he’s had a great season and been a first-choice pick for us.”
Saracens are bidding to retain the Champions Cup after defeating Racing 92 in last year’s final.
Maitland, 28, was named on Monday in new national coach Gregor Townsend’s first Scotland squad for the summer tour which kicks off on 10 June against Italy in Singapore. The Scots also face Australia in Sydney and Fiji in Suva on 17 and 24 June, respectively.