Canada's top military official has apologized for a decision which delayed the repatriation of a fallen soldier and reportedly prevented some of her fellow soldiers from taking part in the ceremony.

In a statement released Thursday afternoon, Gen. Walter Natynczyk, Canada's chief of defence staff, also offered the family of Trooper Karine Blais his "deepest support" during their time of grief.

"I want to offer my sincerest apologies to anyone who may have been offended by the decision to return troops to Ottawa prior to the final repatriation of our fallen comrade Trooper Karine Blais," added Natynczyk.

The comments followed a controversial -- and unusual -- decision to first drop off 117 soldiers at CFB Uplands near Ottawa before bringing Blais' remains back to Trenton for repatriation.

The 21-year-old soldier was killed in Afghanistan on Monday in a bomb blast.

"Having personally attended many Repatriation Ceremonies in Trenton, I can assure all Canadians that our goal is to treat all fallen soldiers with treated with respect, dignity and honour and it is our intention to continue to ensure this policy is followed," said Natynczyk.

Earlier in the day, the military told CTV News the flight plan was a logistical decision, due to the fact that the soldiers were also onboard as part of a troop rotation.

The military decided it would be prudent to drop the soldiers off first in Ottawa, making it easier to transport them to their various home bases, instead of landing in Trenton and then having to take a three-and-a-half-hour bus ride to the capital.

"Sure enough, the 117 soldiers got off the plane (in Ottawa) and it turns out that the flags were not lowered at the Uplands airport," reported CTV's deputy Ottawa bureau chief Rosemary Thompson on Thursday afternoon. "Many of the soldiers on board wanted to go to Trenton."

A military source told CTV News that one official had ordered the Ottawa stop because he did not want the soldiers to spend extra time in transit. Officials from the air force reportedly objected to the order but were overruled.

After the Ottawa stop, Defence Minister Peter MacKay and Gov. Gen Michaelle Jean were among those present in Trenton for the repatriation ceremony.

Still, some soldiers who spoke with CTV expressed disappointment that they would not be on the tarmac when the repatriation ceremony took place.

"Some of us talked about it on the flight last night and none of us would have minded stopping in Trenton first," one soldier told CTV.

"I think they had their flight plans in and that was what they wanted to do ... Unfortunately, as nice as it would have been to be at the ... ceremony in Trenton, we got dropped off here first -- and it's going to be a little tough coming all the way with her and not being with her when she comes off the plane."

CTV also received an email message from a soldier serving in Afghanistan complaining that Blais wasn't being treated with proper respect. Blais' coffin should have been the first thing to come off the military plane, said the soldier.

But because of the troop rotation, there would have been hundreds of pieces of baggage that would be hand-carried, and moved around and over the casket upon disembarking in Ottawa.

While some military observers told CTV it's a minor controversy that is being blown out of proportion, others who were watching the repatriation at Trenton were clearly upset at the decision -- saying if it was made to save cost and time, it was the wrong decision.

"My feeling is, they left with her from Afghanistan, I know it's a long haul -- they've been sitting there on this airplane and everything, but I think they should have come all the way with her (to Trenton)," said Kathleen Paul, a military mother whose son has been on two tours to Afghanistan.

"Blais had gotten killed over there. She was over there the same as them, and they should have come with her. Normally they all stick together," said Paul.

Retired Canadian military Col. Michel Drapeau said the detour is "a sign of huge insensitivity to the feelings of soldiers first of all, and ... more importantly, to the dead soldier and their family."

Drapeau told CTV's Power Play Thursday that the purpose of the flight was to bring home the fallen soldier and to give her family a chance to receive her with respect.

Instead, the coffin sat in Ottawa for three hours and then had a lonely flight back to Trenton, said Drapeau.

"This is not in the best tradition of the military."