No explanation has yet been given for the disciplinary action but it means he will miss Edinburgh's Challenge Cup match with Krasny Yar on Saturday, as well as the Dark Blues' international clashes against Samoa, New Zealand and Australia.
The 29-year-old was born in New Zealand and made more than 50 appearances for both the Highlanders and Southland Stags.
He joined Edinburgh in 2015 and committed his international allegiance to Scotland and has 16 caps, including three at the 2015 World Cup.
In a statement, the SRU said: "Scottish Rugby and Edinburgh Rugby confirm Scotland international and Edinburgh forward, John Hardie, has been suspended from duty pending an internal investigation.
"As a result the player will not be available for selection for Edinburgh, or the Scotland National Team. It is normal practice with such matters that we are unable to comment further given the nature of the investigation."
Hardie was born in New Zealand but qualifies for Scotland thanks to his Fifer grandmother. He has won 16 caps since making his international debut in 2015, including three appearances at that year's World Cup.
He was part of the Edinburgh team which beat London Irish 37-14 last weekend. The news of his suspension comes as another frustration for Townsend, who has already seen skipper Greig Laidlaw and hooker Fraser Brown ruled out of next month's Tests through injury.