During his time with the MST, Mr Rainha had close links to the former President, Luiz Inacio Lula da Silva, whose party the landless movement supported.
The MST said it would not comment on the arrest of Mr Rainha as he "had not participated in any of the national, state or local meetings of the movement" for years.
They accuse the landless group Mr Rainha was leading in Pontal de Paranapanema of channelling money from the government's National Institute for Agrarian Reform away from the landless families for whom it was intended.