Fletcher said that Scotland, who held on at 0-0 until the 69th minute, tried to play on the break but were beaten by a "world-class" team.
"The lads are bitterly disappointed with the result and having worked so hard, the lack of concentration has cost us," Fletcher said.
"Belgium are a counter-attacking side. International football is about tactics and if we went to attack, we would have lost five or six nil. We tried to win the game by hitting them on the counter. The damage was done before we got out here.
"It was always going to be difficult, they are a world class side. The players work [hard for] and believe in Craig Levein and I hope he continues. Qualification looks difficult now but we can still progress as a team."
Scotland are the only team in Group A without a win in qualifying so far and are bottom after four games.