Hamilton suffered concussion while the Glasgow 2014 official suffered a suspected broken collarbone in the accident.
The velodrome had to be closed for 30 minutes, delaying a visit from the Prince of Wales and Duchess of Cornwall.
A Team Canada statement read: "Nic has been assessed by Canada's medical staff and does not have any serious injuries other than his concussion.
"As per concussion treatment protocol, he will not be able to compete for at least seven days, which forces his withdrawal from the track events at the 2014 Commonwealth Games in Glasgow."
Reports claimed the female official was knocked unconscious by the force of the collision. Track cyclists can hit speeds greater than 40mph.
The website Canadian Cyclist, which had an eyewitness in the Velodrome, reported: "Hamilton hit the female marshal straight on and flipped over her in the air, landing on his back and sliding down the track.
"Canadian staff, including the team doctor, plus event medical staff, were with both Hamilton and marshal immediately. Hamilton, after lying on the track with some disorientation, was able to walk off the track under his own power. The marshal required extensive assistance, which kept the track closed for almost 30 minutes, and was removed on a backboard."
Team Canada outlined the circumstances in their own statement, adding: "While training today at the Sir Chris Hoy Velodrome in the Emirates Arena, Canadian track cyclist, Nic Hamilton suffered a concussion after inadvertently colliding with a technical official on the track during a 500-metre effort.
"As far as we can ascertain, neither party was behaving in a manner that breached any training or officiating protocol.
"The official involved also appears to have suffered a concussion, as well as a possible broken collarbone. No other individuals were affected by the incident."
Hamilton will miss out on the 4,000m team pursuit and the 40km points race but his Commonwealth Games might not be completely ruined as he is also entered in the road race on the final day of Glasgow 2014, on August 3.
The statement added: "His condition will be assessed daily by medical staff, and a decision regarding his participation in the road events will be made at a later date.
"Both Nic and Cycling Canada express their concern for the official involved and hope they recover quickly."
Games organisers would not give out any details on the injured official.
A Glasgow 2014 spokesperson said: "A training accident on the Velodrome track required the track to be cleared and medical checks to take place."