Captain Cowan strained his right elbow when trying to push off a Brumbies player early in the match last Friday night and was forced to leave the field.
About 15 minutes later, Mackintosh, who had taken over as captain from Cowan, was forced from the field with injury to his left knee.
He had strained his meniscus behind the knee.
Both players had their injuries strapped yesterday as they sat out training.
Moore said it was too early to say whether the two players would be ruled out and they would have to wait a couple of days to see if the injuries settled down.
"We know enough that there is no structural damage for either of them.
"We'll just have to see how they wash up in the next couple of days," Moore said.
Other players had the usual bumps and bruises but he was confident everyone except lock Tom Donnelly, who is recovering from a thumb injury, will be available for Friday night's match.
First five-eighth Mathew Berquist is on compassionate leave with his sick mother and is unlikely to be available for Friday night.
Moore said he had looked back at Friday night's heart-breaking loss to the Brumbies, and said the attack had worked quite well.
But he had been disappointed with some of the defence, with the Brumbies scoring two tries from relatively simple moves.
Training yesterday morning concentrated on how to combat attacking moves used by the Brumbies and likely to be used by the Hurricanes.
Moore said he told the players the Hurricanes were unlikely to play that badly again, after losing 26-22 in a disappointing display against the Waratahs in Wellington.
