Galagodaatte Gnanasara's Buddhist Force party said the monk, who is wanted in connection with recent arson attacks against mosques and Muslim-owned businesses, had feared he could be assassinated.
"The monk is at a secret location," Buddhist Force (BBS) spokesman Dilantha Vithanage told reporters in Colombo.
"We have told him not to venture out as he could be assassinated after he is arrested."
The party denies orchestrating the attacks against Muslims, who account for just 10 percent of the country's 21 million people but are a formidable political force.
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He already faces charges of contempt for causing a disturbance inside a court.
Sri Lanka suffered its worst religious violence in decades in mid 2014, when riots left four people dead.
The BBS was accused of instigating the violence, but the then government of former strongman president Mahinda Rajapakse did not prosecute them.
Rajapakse's brother Gotabhaya, a former defence minister, was said to be close to the party.
A new government has since been elected and this week it debated the latest wave of anti-Muslim attacks and ordered tough action to prevent an escalation.