Canadian Special Operation Forces soldiers are halting their “advise-and-assist” co-operation with Iraqi and Kurdish troops under Operation Impact, the U.S.-led multinational coalition that has recently made significant inroads against ISIS strongholds in the region.

Canada’s decision to stand down comes amid escalating tensions between Irbil and Baghdad following the Kurdish “yes” vote on autonomy from Iraq last month. The controversial independence referendum has caused a rift between the one-time allies against ISIS, and put foreign coalition partners in the awkward position having to navigate regional politics.

Canada has worked with Iraqi and Kurdish Peshmerga forces in an “advise-and-assist” capacity as part of Operation Impact since joining the coalition to defeat ISIS in 2014. The mission was to train both to be more effective against ISIS, and provide them with real time battlefield strategy.

About 200 Canadian special forces soldiers active in the training and assistance of their Iraqi and Kurdish counterparts have been told to sit tight as a result of Friday’s decision to temporarily suspend operations.

“The situation on the ground in Iraq is fluid, and we will continue to assess our partners’ needs as the situation evolves,” National Defence Minister Harjit Sajjan’s spokesperson, Jordan Owens, said in an emailed statement to CTV News.

Former Commander of NATO Forces in southern Afghanistan Maj.-Gen. David Fraser said putting special forces co-operation on pause should not be interpreted as a sign of wavering support for the coalition, or the battle against ISIS.

“The mission carries on. The intelligence piece carries on, the fighting against Daesh, what we are providing the rest of the coalition (and) the Iraqi security forces, all that carries on,” he told CTV News Channel.

While Ottawa’s decision came as a surprise, some observers in the region have long expected the two sides would clash over Kurdish independence.

Iraqi Prime Minister Haider al-Abadi has demanded the annulment of the vote and the transfer of border control and other infrastructure to federal forces.

Tension erupted into violent clashes earlier this month when Iraqi government forces retook the disputed city of Kirkuk, and other areas outside the autonomous Kurdish region, that the Kurds had seized from the Islamic State group.

On Friday, al-Abadi issued a 24-hour suspension of the movement of troops deployed in Iraq's north to bring territory held by Kurdish forces back under federal control.

Canadian special operations troops will remain on base in the region until the situation stabilizes.

Fraser said the question of who will claim the territory abandoned by retreating ISIS fighters is not one to be answered by Canadian soldiers. He called the decision to temporarily sideline the special forces “quite reasonable and not unanticipated.”

“When they figure it out, we’ll be back,” he said. “They’ve got to figure out how they are going to sort themselves out, and we don’t want to get in the middle of that.”

Offering tactical training and assistance is only part of Canada’s broader mandate under Operation Impact. The rest of the anti-ISIS mission, including a field hospital in northern Iraq, tactical helicopters, refueling for coalition jets, and intelligence contributions, will continue without interruption.

The mission is slated to run until 2019.

With a report from CTV’s Mercedes Stephenson in Ottawa and files from The Associated Press