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The Czechs took the lead in the 11th minute, Martin Erat slapping the puck through the goaltender's legs from distance.
Controversy then struck just a few minutes later when Janis Sprukts's shot saw the puck fly into the middle of the goal, hit the in-goal camera and bounce back out.
No Latvian players celebrated, and play continued for a couple of minutes before finally the officials were alerted, watched the video replay and awarded the goal.
The win was the first of the three-game preliminary round for a Czech team looking to return to the Olympic podium for the first time since winning the bronze medal at the Turin Winter Olympics eight years ago.
They lost their first game 4-2 to Sweden two days ago, and will be in action again tomorrow against Switzerland.