The Bulgarian Interior Minister Mladen Marinov described the murder as "exceptionally brutal" and said Marinova was raped before she was murdered, according to state media. "He has been charged in absence for two crimes - rape and premeditated murder with extreme cruelty", Tsatsarov said.
Marinova hosted a show last month featuring two investigative journalists who were detained for their work on suspected fraud involving European Union funds. Her body was found dumped near the Danube River in the town of Ruse, northern Bulgaria, on Saturday. In August 2017, Swedish freelance journalist Kim Wall was reported missing and found murdered in October when she was researching a story on Danish inventor Peter Madsen.
"We have collected a lot of evidence which for the time being suggests that the person is guilty". "But we are continuing to look at all hypotheses".
The country's chief prosecutor, Sotir Tsatsarov, said he could not yet say whether Ms Marinova's death was linked to her work.
Viktoria Marinova, 30, is the third journalist to be murdered in the European Union in the previous year and the fourth since the start of 2017. Caruana Galizia was killed in a vehicle bombing in October in Malta and Jan Kuciak was murdered in Slovakia in February.
"In just three days, I've read monstrous things about Bulgaria. None of them true", he told a news conference. "Bulgarian authorities must employ all efforts and resources to carry out an exhaustive inquiry and bring to justice those responsible", the media watchdog said in a statement.
European Commission vice president Frans Timmermans had been among the first to suspect a political motive.
Journalists' groups and European leaders expressed shock at the murder.
Prime Minister Boyko Borissov offered condolences to her family and thanked investigators for their work. "Again a courageous journalist falls in the fight for truth and against corruption", he tweeted Sunday, not long after the news of the murder broke.
He quoted Mr Juncker as saying previously that "too many" journalists are being intimidated, attacked or murdered and "there is no democracy without a free press".
Flowers and candles are placed in memory of Bulgarian TV journalist Viktoria Marinova in Ruse, Bulgaria, October 9, 2018.
Thousands of Bulgarians held commemorations on Monday evening with the largest crowds turning out in Ruse where the crime took place, according to Balkan Insight.
Violence against women has also been widespread in Bulgaria and the Bulgarian Helsinki Committee rights group said 19 women have already been killed in the country so far this year as a result of abuse.
Bulgaria ranked 111 out of 180 countries in the Reporters Without Borders world press freedom index this year.