Glasgow Warriors, who are run by the Scottish Rugby Union, and Edinburgh Rugby, who became a franchise this season, continue to function on a professional basis.
However Borders bit the dust after a 24-16 defeat to the Ospreys, who clinched the Magners League title at Netherdale.
Capped 82 times by Scotland, 34-year-old Townsend regrets the SRU moving in March to shut down Borders.
"Obviously it was their decision to cut a third team and to disband us, but who's to blame? Who knows?" Townsend told BBC Radio Scotland.
"The product has not worked across the board in Scotland ... professional rugby, the crowds aren't great.
"I think it's a cultural thing that we haven't got into professional rugby as a nation, as a union, like the Irish have and the Welsh are now doing.
"But I do think that three teams is the minimum necessity if we're going to have a successful international side, so I really hope that one day there'll be a third team.
"Fingers crossed it will happen next season, somewhere else in Scotland."
Considering Scotland finished bottom of the recent RBS 6 Nations Championship, their stock can fall little further, however an extended spell of mediocrity could leave the national team lagging well behind their northern hemisphere rivals.
Townsend, who will begin a new role with the Scottish Institute of Sport Foundation later this year.