Macclesfield will investigate the incident when play was suspended in the FA Cup draw with Walsall after a number of balls were thrown on to the pitch.
Players had to kick the balls clear of the pitch
About 20 balls were launched from outside the club's Moss Rose stadium, landing at the Star Lane end.
Chief executive Patrick Nelson told BBC Sport: "We were completely surprised. I was sitting behind the chairman and we were both rubbing our eyes.
"At the moment we have no idea where they came from. We know nothing."
The unusual incident during the 0-0 draw is thought to have been initiated by pranksters, although no-one has yet claimed responsibility.
"It might bring a wry smile to people's faces but we had TV cameras here for the game and we wanted to put our best face on," added Nelson.
"That's not what we wanted.
"But it is a difficult thing to investigate. Where do you start?"