Assistant referee David Bryan was hit by a flare thrown from the Tottenham supporters' end during their match against Aston Villa at Villa Park on Sunday.
He was struck on the back of the neck moments after Andros Townsend gave Spurs the lead in the first half.
He was able to continue without treatment, though smoke from the flare delayed the restart of the game.
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."
West Midlands Police have arrested two men aged 25 and 47 over the incident.