They say they were restrained, doing only what they had to, but Amnesty International says they 'treated everyone violently'.
Indonesia's disputed election is now in the hands of the country's top court, following a challenge by the defeated candidate on Saturday.
At least seven people have been killed in clashes between opposition protesters and police since Tuesday.
And there are now calls for a formal investigation into how police handled the situation.
Al Jazeera's Andrew Thomas reports from Jakarta.
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