"Eleven suspects were arrested and searches are ongoing on several locations" including in the capital Sarajevo and other towns, a police statement said.
The state prosecutor's office said those arrested were suspected of "having financed terrorist activities, organising terrorist groups or illegally joining foreign paramilitary formations."
Among the arrested, several are suspected of "fighting alongside radical terrorist groups and organisations" in Syria or Iraq last year, it said.
The arrests today were the second part of a security operation - dubbed "Damascus" - launched in September. At the time 16 suspected jihadists were arrested of whom five remanded in custody.
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Around 150 Bosnian citizens have joined Islamist groups fighting in Iraq and Syria and some 20 have been killed there, according to officials' estimates.
Bosnia's Muslims, who make up 40 per cent of the country's 3.8 million inhabitants, mostly practise a moderate form of Islam.
However, during the 1992-1995 war between Croats, Muslims and Serbs, a large number of Islamic volunteers came to Bosnia and many stayed on in the country.