Assistant referee David Bryan was hit by a flare thrown by a Tottenham Hotspur supporter during their game against Aston Villa.
England winger Andros Townsend gave Spurs the lead just seconds before the incident in which the flare struck Bryan in the neck.
The restart of the game was delayed, yet fortunately for Byran he did not need treatment and carried on with ease for the rest of the match.
Tottenham manager Andre Villas-Boas said: "It is not great to see. It should be avoided completely. It touched the linesman and situations like this don't have a place in football. I sincerely hope it doesn't happen again."
A Football Association spokesman said: "The FA will investigate this matter, which is unacceptable. We will await the match officials' report and will be speaking to the clubs. Such incidents highlight the dangers of pyrotechnics being used in a football stadium."
Although Bryan was not injured, throwing flares is a serious thing, with Damien Green, policing minister, warning that flares were putting the lives of other supporters at risk.
In a match between Aston Villa and Wigan last season, one boy suffered lung damage, with he and two other women hospitalised. The match finished 2-2.
A flare can stay at the temperature of 1,600 degrees Celsius for up to an hour, reinforcing how dangerous it can be. In South America, one boy was killed by a flare thrown by supporters during a cup match in Bolivia.