Henderson, who won gold for New Zealand on the track at the 2002 Commonwealth Games, is also said to have posted another controversial tweet, which read:
"I am so sick of it. It becomes common knowledge within days. Why try cheat."
The Astana team reacted angrily to the outburst, with coach Paolo Slongo intimating Aru could take legal action over it.
Aru's agent Alex Carera also waded in, according to roadcycling.co.nz.
"A famous athlete like Greg Henderson who has 30,000 followers on Twitter can cause huge damage to a person like Fabio, his Astana team, and the sport," said Carera. "Our lawyers will look at what has happened and consider where to start legal action."
Henderson has since apologised for his comments by posting the following message on Twitter:
"When you are sick. You are sick. Jumping to conclusions helps nobody. My mistake @FabioAru1. I should shut my mouth. Sincere apologies."