Boyle, who appears on Channel 4, which is broadcasting the games, has already drawn condemnation from many Twitter users, including Olympic medallist Lizzie Armitstead, who said: "Frankie Boyle isn't funny."
The comedian joked that the Saudi Arabian team are "mainly thieves", referring to how some criminals have had their hands removed for stealing.
He also made comments about referees in blind football.
In 2009, Boyle was censured by the BBC Trust for comments about Olympic swimmer Rebecca Adlington, following her gold-winning success at Beijing the previous year.
His remarks were ruled to be offensive but no further action was taken, which prompted her agent to complain about the "slap on the wrist".
Boyle returned to Channel 4 – the official Paralympics broadcaster – earlier this week with The Boyle Variety Performance.
Previous series Tramadol Nights prompted more than 500 complaints after he mocked Katie Price's disabled son.
A Channel 4 spokesman said: "Frankie Boyle was tweeting from his personal account and not on behalf on Channel 4."