“We learned that someone pirated the site,” the panel’s head Beatrice Atallah told reporters.
State radio was to continue announcing results, but at a slow rate that has prompted criticism in the vast Indian Ocean island nation.
Results from a little more than a quarter of the polling stations show Robinson Jean Louis, the candidate backed by exiled former president Marc Ravalomanana, in the lead with nearly 29 percent of the vote.
Hery Rajaonarimampianina, thought to be the favourite of current strongman Andry Rajoelina, was second with 14.4 percent, with another 31 candidates trailing far behind.
The polls were a first step for the island to return to democracy after interim leader Rajoelina seized power in 2009, provoking its suspension from international bodies and a freeze in foreign aid and investment.
Both Rajoelina and Ravalomanana were barred from running in the poll after intense international pressure.
A second round is set for December 20 along with legislative polls.
