Bolivia's attorney general has announced an investigation into leftist former president Evo Morales, alleging his involvement in the murder and torture of European citizens in 2009.

Seventeen years ago, police raided a hotel in the city of Santa Cruz, shooting dead Eduardo Rózsa Flores, a Bolivian-Croatian, Michael Dwyer, an Irishman, and Árpád Magyarosi, a Hungarian-Romanian.

Bolivian-Croatian citizen Mario Tadic and Elöd Tóásó from Hungary survived and reported being tortured after their arrest.

The Morales administration in power at the time claimed that Rózsa Flores was leading efforts to promote a separatist movement, with funding from the rightwing economic elite of Santa Cruz.

Acting attorney general José Armando Urioste announced the preliminary investigation into Morales just one week into the job on Monday.

In a letter to the supreme court, Urioste said authorities were gathering evidence against Morales and his former vice-president Álvaro García Linera "for the alleged commission of the crimes of murder, abuse, torture and unlawful detention".

The investigation comes after a complaint filed by rightwing lawmakers Tomasa Yarhui and Rodrigo Antonio.

When the raid occurred, Morales told the press during an official visit to Venezuela that he had ordered the detention of the foreigners, whom he called "mercenaries".

Neither of the accused has commented on the latest inquiry.

Morales, the first-ever Indigenous person to lead Bolivia, is currently in hiding from two active arrest warrants against him. One relates to his alleged role in massive protests that paralysed the country for 53 days earlier this year. The other accuses him of trafficking a minor with whom he is said to have had a daughter. Morales denies the allegations.