Frustrated head coach Schmidt conceded Ireland made no progress from their Samoa victory in their 32-15, four-try defeat to Australia on Saturday.
The former Leinster head coach was angry with his side for gifting Australia's back-three too many counter-attacking opportunities, leading directly to tries for Michael Hooper and Nick Cummins.
Admitting Ireland are still a "work in progress", Schmidt confirmed 28-year-old Sexton must wait for scan results on Monday to discover the extent of his hamstring problem.
Schmidt explained: "He has a hamstring injury, we're just sure of the extent of the injury at the moment.
"To be honest it's too early to tell. He felt it wasn't particularly bad and he pulled up quickly.
"But it's out of our control, we just have to wait and see what happens and wait for the results of the scans.
"We'd given Jonny a weekend off and a refresher and we thought we'd get two big weeks out of him, so it's really disappointing.
"Rob Kearney's not too bad after his knock, someone just landed on his rib and he was sore from something he picked up last week.
"We're pretty hopeful he'll be available for next week."
Australia flanker Hooper claimed a brace of tries, with Quade Cooper stealing in for a cheap score when replacement Ian Madigan and Luke Marshall completely missed him as he ghosted through the midfield.
Cummins finished the other, with Schmidt finding no argument with the loss - citing a "disconnect" between his off-kilter players.
"I'll put a few fingers in a few different spots to be honest," he said.
"I thought there was a fair bit of defensive naivety, but I did think we came back into the match extremely well.
"It was very hard to get them off the ball, and that made it extremely difficult to get onto the front foot. One of the things that would account for that, Jonny Sexton hadn't trained a lot.
"Ian Madigan didn't really get much of a look-in and then was expected to run the show for the second half. That was a big ask, particularly when they were getting off the line so quickly.
"Because we were squeezed for space we didn't get to pick our kicking options, and that forced us into problems.
"In a game seldom does everything go according to plan, and you've got to be adaptable enough to cope.
"And we undid ourselves at times as well, Conor picked the ball out and one of our own players held onto it. That's part of the disconnect we've got really at the moment.
"I don't think we're any further forward than we were last week after Samoa, and that's a big disappointment, because we want to keep making progress week to week."
Ben Mowen admits Australia are desperate to overturn northern hemisphere criticism of the Wallabies' scrum.
Number eight Mowen was impressed with Australia's four-try haul, taking their tally to 23 scores in their past five Tests, but the 28-year-old was equally proud of denying Ireland a try of their own.
And he believes it is time wider perception on the Wallabies' scrummage changed.
"We haven't been happy with the criticism that's come our way because we've got a great scrum," Mowen said.
"To do what we did at the end with seven blokes, after the red card for Tevita (Kuridrani), that was great. It's giving us a great platform.
"There's a willingness to scrum, we want to create that platform, and we're making it happen.
"I don't think if you ask many blokes up here they'd rate our scrum, but that's why we want to leave this tour having given a different impression of that.
"We've got guys who can really go well in that area and that's something we're passionate about doing."
Australia head coach Ewen McKenzie suggested the apparent northern hemisphere fixation with winning scrum penalties can hinder attacking opportunities.
McKenzie said: "We like to scrum to play: other teams like to scrum to win penalties.
"We've given ourselves good platforms to play from our scrum, and that's what we want. We were able to put a bit more pressure on the opposition, win some more penalties and gain from that."
Australia remained on the pitch at half-time, running through their team talk and second-half preparations.
McKenzie said that will continue to be the norm for his side, who registered back-to-back victories for the first time in 2013, following their 50-20 Italy win.
He added: "We enjoy staying out there, I've said many times that's how the game was designed.
"We've stayed out and had oranges for 100 years.
"We stay in the moment and the ambience out there, and we get through more by staying out.
"Some of the grounds there's a lot of distance to cover to the dressing rooms, so we actually get more done by staying out."