Graziano Pelle scored the winner 12 minutes into the second half, but the scoreline should have been far more comfortable for Italy, who dominated possession in Malta and squandered numerous first-half opportunities.
"We put a lot of effort in but the pitch was in terrible condition and that did not help," Conte, who will name his 23-man Euro 2016 squad this week, told Rai Sport.
"We must keep working. I liked the application and effort of the boys - we know there is a lot of work ahead of us.
"I am not a magician, so I don't know what we'll have when we get to the first game of Euro 2016.
"Let's look at the fact we didn't concede any goals and that Scotland didn't had a shot on target.
"Let's look at the positives and not always everything negative."
Goalscorer Pelle added: "We were not at our best but I'm happy that I scored. We should have created more in the second half."
Italy face Finland in their final pre-tournament warm-up on June 6, before kicking off their Euro 2016 campaign against Belgium a week later.