It came after last Friday's closing of nominations for the 2021 general election.
The seats, Faleata urban and Salega East, had been held by Olo Fiti Va'ai and Faumuina Wayne Fong.
The pair had breached parliamentary standing orders on switching allegiance to become candidates of the newly formed Faatuatua ile Atua Samoa ua Tasi, or F.A.S.T, political party, for next year's general election.
The MPs have publicly revealed the Speaker's decision after the sergeant at arms of Parliament delivered them a letter.
The chairman of the F.A.S.T party and MP, Laauli Leuatea Polataivao Fosi, has said the Speaker's decision will be challenged in court.
No by-election will be called for the two vacant seats because there's less than six months remaining of the current parliamentary term.