Police Inspector-General N. K. Illangakoon said the new unit would swiftly investigate any complaint relating to "religious matters" on the majority Buddhist island amid rising tensions over the attacks.
"This unit will cover the entire country and deal with complaints relating to religious matters," Illangakoon told reporters.
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The move follows a series of attacks since early last year on mosques, churches and Muslim-owned businesses by nationalist Buddhist groups who accuse religious minorities of undue influence on the island.
Videos shared on YouTube have shown mobs led by Buddhist monks throwing stones and smashing a Christian prayer centre in southern Sri Lanka in January this year while police looked on.
Senior Buddhist monks have also been caught on video threatening violence against their moderate colleagues who advocate religious tolerance.
Moderate Buddhist monks and Christian and Muslim leaders have accused police of failing to prosecute those behind the attacks.