"We were just not happy with the way he was trotting on right-handed tracks," Sean McCaffrey, his Cambridge trainer, said.
"We had X-rays done and found a change of bone density in his off front pastern."
McCaffrey said Sovereignty could have raced at the Harness Jewels meeting at Ashburton on May 30, but it was decided to take a conservative approach.
"He is too good to risk at his age and we have accepted the veterinary advice to box him for three weeks and give him three months off work," McCaffrey said.
Sovereignty, who last raced on April 3, has won three of his 10 starts and placed in another three this season for $77,209 in stakes.
He won the 3yr-old division of the Harness Jewels at Cambridge last season in a New Zealand record time of 1.56.9 for the mile.
The Monarchy gelding won eight of his 12 starts at three and $202,527 in stakes for Cambridge owners Charlie and Annette Hunter.
The withdrawal of Sovereignty has left Leighton Hest the top Harness Jewels qualifier on stakes earnings for the 4yr-old trotters.
The Phil Williamson-trained Leighton Hest has six of his seven starts and $55,562.
Maximillion, winner of five of his 10 starts this season, will miss the Harness Jewels division for 4yr-old pacers.
"He has filling in his off front leg and we have turned him out," Gerard O'Reilly, his trainer, said.
"He had a similar problem after his first three races and recovered after three weeks but we decided on a decent break."
•Rocket Beebee qualified as a pacer 7.8sec inside the required time at Gore yesterday.
He is a 3yr-old by Pacific Rocket from Rosie Franco, trained by Murray Brown.
Results of trials at Gore yesterday:
Weather, fine; track, fast.
Two-yr-old pacers, mobile, 1700m: Royal Stripper K Barclay 1; Our Life 2; Paul Senior 3. Three started. 4L, 1 1/2L. Time, 2.12.6. Trainer, D McLachlan.
Qualifying test, pacers, mobile, 2200m: Cool Jaccka A Armour 1; Hawaii Five O 2; Falcon Green 3. Three started. 1 1/2L, 2 1/2L. Time, 2.51.4 (three qualified). Trainer, M Brown.
Qualifying test, pacers, 2200m: Rocket Bebee 1; Doves Patch 2; Washington Hotshot 3. Six started. 5 1/2L, nk. Time, 2.50.5 (six qualified). Trainer, M Brown.
0w pacers, 2200m: Elusive Courage B McLellan 1; Victor Vtoo 2; Robyn Maree 3. Four started. 1L, 1 1/4L. Time, 2.55.7. Trainer, M Hunter.
0w pacers, mobile, 2200m (first heat): Three's Company C Barron 1; Magnetic Lone Star 2; Vitalizer 3. Six started. 10 1/2L, 2 1/4L. Time, 2.48.8. Trainer, C Barron.
Second heat: Birchwood Jack A Suddaby 1; Nicola Jaccka 2; Fire Fighter 3. Four started. 1/2L, 2L. Time, 2.52.2. Trainer, T Barron.
1-4w pacers, mobile, 2200m: Gold Art T Barron 1; Silver Ranger 2; Karackas 3. Nine started. 1L, 2 1/4L. Time, 2.46.5. Trainer, T Barron.
•James Burke is now in the Blenheim stable of Pat and Mike O'Brien after a change of ownership. The Artiscape 5yr-old won two races when trained at North Taieri by Martin Denton.
The 2yr-old Lots More Grins has been sold to Australia.
The Grinfromeartoear colt was placed at Wyndham and Winton from four starts for Invercargill trainer, Colin Devery.
•Devil Moon, winner of the group one Turnbull Stakes, was bought for $775,000 by Patinack Farm at the Sydney Easter sale, AAP reports.
Belong To Many, the winner of seven races and 12 times placed in 27 starts, was sold for $A525,000.
Belong To Many was bought by Vin Cox Bloodstock.
Trained by Barbara Joseph, Belong To Many was named for the 800 people who took shares in her syndication.
She was offered for sale with the expiry of the three-year racing lease.
She ran second to Court in the Sapphire Stakes last Saturday.
She has earned prizemoney of almost $A450,000, a substantial return on her $A20,000 yearling price.
Happy Heart, the dam of 2007 VRC Oaks winner, Arapaho Miss, was sold for $A375,000.