Carlton were downed 0.16.13 (109) to 2.7.9 (69) by Brisbane at Etihad Stadium on Friday night, bringing a flat end to what had been a promising first pre-season campaign under Malthouse.
The three-time premiership coach labelled the performance terrible, saying his players lacked competitiveness and surrendered too easily, giving up nine goals to one in the second half.
But while maintaining the Blues have made some decent progress over the off-season, Malthouse said it was always going to be a long process.
"We need to reassess what took place in the last two weeks and work on it for the next two or three months and see if we can iron a few of those things out," the veteran coach said.
"Two or three months takes you into the season ... if it means eating into (games against) Richmond, Collingwood, West Coast, Geelong and whoever else is next, then so be it.
"That's got to be the case. We've just got to keep honing those skills under this sort of pressure."
Malthouse said he was a realist and had never expected to transform the Blues instantly.
He had no explanation for Carlton being thrashed 19-7 in centre clearances, an area they had previously performed well in, despite comfortably winning the hit-out count.
Carlton's attack is also a worry without the injured Jarrad Waite - who's not expected back for their opening round clash with Richmond - with the Blues' other key forward options failing to fire.
But Malthouse said the Lions' defence would make life difficult for all key forwards this year.
One positive was that midfield star Chris Judd made it through his first game of the pre-season, after a hamstring injury, although he had little impact.