"FIFA and the ethics committee are committed to have zero tolerance for any breach of the code of ethics and the bid registration," football's governing body in a statement on Monday.
"FIFA and the ethics committee are determined to protect the integrity of the 2018 and 2022 FIFA World Cup bidding process."
Zen-Ruffinen, general secretary from 1998 until he left football's governing body in 2002 after accusing FIFA president Sepp Blatter of mismanagement, later called for an external investigation into alleged corruption.
Last week, two members of FIFA's executive committee members were provisionally suspended on suspicion of selling their votes in the contest to host the two tournaments.
Nigerian Amos Adamu and Tahiti's Reynald Temarii were banned from all football-related activity for 30 days while FIFA's own ethics committee investigates allegations they offered to sell their votes when approached by Sunday Times journalists posing as lobbyists for an American consortium.
FIFA, which hopes to conclude the investigation by mid-March, confirmed that it would include Zen-Ruffinen's comments in its investigations.
"FIFA will provide all of the information collected on this matter to the ethics committee," FIFA said.
"FIFA has immediately requested to receive all the documents and potential evidence that the newspaper has in relation to this matter, and will in any case analyse the material available.
