The home side scored seven tries to two and led 28-5 at half-time, scoring two tries near the end of the game to inflate the score.
Wellington gave the ball plenty of air, and was powerful at the breakdown in fine conditions on a spongy field at Porirua Park.
Martin, although not happy with the loss, said it was an improvement in intensity from last week, and he was pleased with the set pieces.
The scrum was strong, and the line-out functioned well.
Southland defeated Otago last week 43-36 at Tahuna Park.
Otago's two tries were scored by winger Lucky Mulipola, one in each half.
Martin said Wellington made the most of an intercept try and the turning over of ball by Otago at critical stages.
Wellington loose forwards Chris Masoe and Serge Lilo were strong at the breakdown and with the ball in hand.
Otago tried out Hoani Matenga on the openside flank and Martin said he showed plenty of energy.
Southern flanker Carl Anderson came on in the second half, and played a solid match, Martin said.
Martin was pleased with the first 25min of the second half when the teams scored a try each.
First five-eighth Daniel Bowden suffered a suspected broken rib after a tackle near the end of the first half, and may be out for three to four weeks.
Players to impress for Otago were forwards Tom Donnelly and Jason Macdonald.
Halfback Alby Mathewson had a strong game while 18-year-old fullback Buxton Popoalii ran hard.
