Dozens of students were demonstrating outside the building in central Jakarta when the blast was heard, said witnesses.
A KPU staff member said the explosion was located near the washrooms on the ground floor of the four-storey building. Police were setting up a cordon around the building which was being evacuated.
The source of the blast was not immediately known and there was no word on injuries.
The students were demonstrating against alleged irregularities in the 5 July poll.
The election results are expected to show that Indonesian President Megawati Sukarnoputri will face her estranged former security minister Susilo Bambang Yudhoyono in a run-off presidential election in September.
The election is being closely watched by allies, such as the
United States, and investors, both concerned about security in Indonesia after it was hit by bombings on the tourist island of Bali in 2002 and at a luxury Jakarta hotel last year.
The first attack killed 202 people, mostly foreign tourists, and the second killed 12.