"The searches were carried out because of suspected practices of tax fraud, criminal association, money laundering, corruption and forgery of documents," the prosecutor's office said in a statement.
Twenty-two teams of detectives fanned out to search club offices and stadiums in Lisbon, Braga and Leiria, as well as private homes, companies and lawyer's offices across Portugal, it said.
A police source told Reuters that the third-tier side Uniao de Leiria, owned by Russian businessman Aleksandr Tolstikov, was at the centre of the investigation in which Tolstikov, another Russian national and two Portuguese have been indicted.
"Other clubs are not under suspicion, but have been searched because they possess some documents that will help the investigation of existing evidence of capital transfers, presumably from Russia and related to criminal activities, for money-laundering in Portugal," the source said.
Neither Tolstikov nor his associates in Moscow and in Portugal answered telephone calls from Reuters. An e-mail sent to Tolstikov's address listed on the website of his D-Sports agency, whose logo appears on Leiria's club jerseys, was returned as undeliverable.
Nobody was available for comment at Uniao de Leiria.
The police source would not say more on how the scheme worked, but some media said contracts involving Russian players were used to launder money.
Tolstikov bought the bankrupt club, which was once coached by Jose Mourinho, in 2014 and last year it had as many as seven young Russian players, although just one in the main squad. At least one has been transferred to Benfica's second team.
(Reporting By Andrei Khalip, editing by Axel Bugge and Richard Balmforth)
