The Blues suffered a first ever defeat to Greater Western Sydney on Sunday, crashing to a 15.10 (100) to 14.8 (92) result that effectively ends their finals hopes for 2014.
What made it even more disappointing for Malthouse is the fact it came on the back of competitive efforts against top-four hopefuls Geelong and Hawthorn over the past fortnight.
Although able to stick with some of the competition's better teams, the Blues have suffered losses to Melbourne, Richmond, the Brisbane Lions and now GWS.
"On the surface, we've played football at the intensity that's required against the top sides," Malthouse said.
"Against sides that are not in the eight, for unknown reasons to me, we do not hold that intensity.
"That is so disappointing. To try to put the finger on what the reason for that is, it's probably a combination of things that makes it happen.
"That's what we have to go through to find out exactly why we can't sustain intensity for a long period."
When it was suggested it was a disappointing display, Malthouse replied: "Good word. I reckon last week (against the Hawks), I was very disappointed for the players.
"This week, I'm very disappointed in us."
Carlton lost skipper Marc Murphy before the game, feeling some hamstring tightness during the final warm-up to be replaced by Dennis Armfield.
Malthouse didn't know if the captain would be available to face Collingwood next week, but didn't feel Murphy's absence had been a major factor against the Giants.
The veteran coach seemed a little lost for answers about the performance, saying the Giants appeared to want the victory more than his troops.
"I'm starting to think just mentally we don't get up for three weeks in a row," he said.
"We may not have won the last two games (against Geelong and Hawthorn), but we countered two top-quality sides in desperation and probably got finished off by better players.
"I'm not saying for one moment Greater Western Sydney aren't a better combination, but they've still got a lot of youth.
"Unfortunately when we needed things to take place on the ground, they weren't taking place, and that gets down to people taking charge.
"The players need to take charge and be responsible for set-ups, the ability to will yourself to win a game.
"The players that willed the victory, unfortunately for us, were all Greater Western Sydney players.
"We had no one there that stood up and took control."
GWS finished on the right end of most statistical categories, including disposals (355-341), contested possessions (150-146), tackles (76-55) and inside 50s (57-50).
Malthouse believed his side lacked the polish and enthusiasm of some of the young Giants.
"The simple fact is they out-ran us, they out-touched us; they're going to be a very, very powerful side when they get a bit more maturity," he said.
"Right now, they've got the ingredients of a very good football side.
"When you look at some of the players in and around the ball, they're good one-touch players.
"We were dreadful in one-touch. Dreadful. We gave the ball back to them time and time and time again.
"And you can't win games of footy when you give the ball back."
Twitter: @AFL_JD