Two goals from Mario Gomez gave Germany a 2-0 lead before Dutch forward Robin van Persie cut the deficit in the 73rd minute with his team's first goal of the tournament.
"We lost against a very good team and if you want to beat this Germany you have to be on top as a team and as players. We weren't today as several players are not really in shape," said Van Marwijk.
"The opening phase was ok but after that it all went wrong in our defence.
"Up front Van Persie did well but our wingers never threatened their defence and lacked pace."
Dutch winger Arjen Robben, facing several of his Bayern Munich team-mates on the Germany side, was also critical of the performance.
"There is no cohesion between our lines. There are gaps and we are not connecting. Then it is very difficult to recover the ball... At this moment we are not steady as a team in the way we were two years ago. There is not one line to blame but we failed as team."
Van Marwijk's team, who lost to Spain in the 2010 World Cup final, now teeter on the brink of elimination after two defeats following their opening loss to Denmark.
"We are disappointed of course that we lost," Van Marwijk said. "We started quite well that is how we wanted to play. The goal from Germany came out of nothing.
"When you lose you have to say you have to be more courageous going forward. Today we weren't strong enough or courageous enough in defence... we didn't have enough one on ones in the middle of the field."
The Netherlands must beat Portugal in Kharkiv on Sunday in their final group game to have a chance of reaching the quarter-finals.