Brig.-Gen. Charles Lamarre, in charge of the task force doing the pullout, told The Canadian Press in an interview that the shutdown is disappointing.
The halt of NATO supply trucks was in protest of a U.S. air strike on the weekend that killed at least 24 Pakistani soldiers along the border with eastern Afghanistan.
It's the largest loss of life in a cross-border raid since the war began and comes amid deteriorating relations between the Obama administration and Pakistan.
The incident also threatens to disrupt an international conference on renewing economic commitments to Afghanistan 10 years after the overthrow of the Taliban.
Getting out of Kandahar by the end of the year was one of the mandates handed to the military by the House of Commons and Lamarre says he is confident the deadline will be met.
Sensitive military equipment and vehicles have already been flown out of the southern Afghan city aboard air force C-17s, beginning in July when the combat mission came to an end, but the Defence Department has relied on a private contractor to move sea containers of ordinary stores over land to the Pakistani port of Karachi.
Lamarre played down the disruption, predicting economic factors would pressure the government in Islamabad to get commerce and people moving again.
"The use of a ground line of communications through Pakistan with a contractor is something we've been using for quite a while. In fact, all nations use it to move material," Lamarre said from Kandahar Airfield.
"The current shutdown is regrettable. Usually because of economic pressure and the desire to have commerce moving, it eventually reopens and we anticipate it will be the case here."
The supply line through Pakistan has long been precarious for NATO, which has seen many of its fuel trucks and flat beds with military vehicles attacked and torched.
Most of the Taliban-led assaults have taken place in the winding mountain roads that connect eastern Afghanistan with northern Pakistani cities, such as Peshawar.
The preferred route for contractors hauling Canadian war material has been directly out Kandahar province to the border at Spin Boldak and south through the city of Quetta, where ruling members of the Taliban are alleged to be hiding.
Officials at the Ottawa-based expeditionary headquarters noted that the current disruption is the first time in memory that the crossing has been closed. At least one Canadian-contracted convoy was held up as it tried to exit over the weekend.
The withdrawal has otherwise gone without hitch, despite the trek through semi-hostile territory.
NATO officials in Kabul, speaking on background, took pains to describe the unfolding border dispute as an "inconvenience," but added the longer it drags on the tougher it will be.
Approximately one-third of the alliance's war supplies come through Pakistan, according to recent published reports and military journals. NATO has been making a deliberate effort to reach landlocked Afghanistan through northern routes in Tajikistan and Uzbekistan.
An investigation into the NATO bombing is underway.
Diplomats quoted in the New York Times say a preliminary review has found a joint NATO and Afghan patrol came under sustained fire late Friday or early Saturday in the border area.
The troops called in air support and claimed they tried to contact Pakistani troops on the other side, believing they were clear to bring in the strikes.