After being unbeaten in 2013, Belgium – who easily qualified for the 2014 FIFA World Cup – finished the year with back-to-back losses.
The latest defeat came in a 3-2 loss to Japan in Brussels on Tuesday, days after being beaten by Colombia.
Wilmots said the next two months would be crucial to his team's chances of being successful in Brazil, but understands he has no control over how often his players get on the pitch.
"It was an excellent year in 2013, but we have ended up losing two games. It obviously does not please us to end the year in this fashion, but I think I know why," Wilmots said.
"We have not lost our playing qualities but sometimes when you do not play a lot for your club, there is a lack of pace and fitness.
"When you are not fully fit, you make mistakes and you do not defend as you would normally defend. I think this is the biggest project for us to do.
"The months of December and January will be very important for the national team, but I have very little influence on the amount of time the players play for their clubs."
Belgium took a 15th-minute lead through Kevin Mirallas, but Japan levelled thanks to Yoichiro Kakitani.
Goals from Keisuke Honda and Shinji Okazaki had Alberto Zaccheroni's men ahead before Toby Alderweireld scored what proved to be a 79th-minute consolation.
Wilmots said he experimented during the clash, one he felt Belgium 'dominated'.
"We tried a new formation tonight, a 4-2-3-1. That meant using Eden Hazard in support of Romelu Lukaku," he said.
"It went well for 20 minutes even if the Japanese were more threatening and had a few free players. However, I felt we had control of the game. We have not conceded opportunities.
"In the first half, the only one chance that Japan had was the one they scored. For the rest, we have dominated and played very well.
"In the second half, I rebalanced and made the substitution of Eden Hazard. This was expected because he has Champions League and (English) Premier League games (with Chelsea) coming up.
"This is a friendly game and I wanted to give playing time and chances to other players so they could try and impress."
