Morsi had about 30 percent of the vote, the officials said.
A number of other candidates were also doing well and no one was expected to collect a majority of votes, which means there will be a runoff in June, Voice of America reported.
Morsi was in a race with former Brotherhood leader Abdel Moneim Aboul Fotouh, former Air Force chief Ahmed Shafiq, socialist Hamdeen Sabahi and former Arab League chief Amr Moussa.
The Brotherhood's Freedom and Justice Party said it expects Morsi to compete against Shafiq, who served as prime minister under ousted President Hosni Mubarak, in a runoff.
A runoff between those two candidates could sharpen the divide between Islamists and what is left of the Mubarak regime, election observers said.
Morsi -- chairman of the Freedom and Justice Party, which controls the Egyptian Parliament -- joined the race late after the Brotherhood's first choice was disqualified.
Observers said participation by women appeared to be particularly strong in the election.