Party delegates voted overwhelmingly to retain Mr Mubarak for another five years in an uncontested secret ballot.
There had been speculation that the congress would elevate the president's son, Gamal Mubarak, to head the party.
The younger Mr Mubarak has often denied that he is being groomed to succeed his father as
The four-day conference is officially to discuss social and economic policy.
But it is the first time the party has held a leadership vote since Mr Mubarak took over after the 1981 assassination of President Anwar Sadat.
Economic reformer
Gamal Mubarak chairs the party's policy committee, giving him the chance to exert considerable influence.
He is credited with the successful economic reforms implemented over the past three years.
In recent years the former banker has come to wield enormous influence over Egyptian affairs, says the BBC's Heba Saleh in
He is admired by many in the business community who praise him as a thoughtful man, attentive to detail and determined to modernize the economy, says our correspondent.
But his critics say he is not a democrat and political changes introduced by his party last year have made
Those who want him as president argue that he would guarantee the continuity of economic reform, and form a preferable alternative to the Muslim Brotherhood.
But those who oppose him say the next president should come through genuinely democratic elections.
PHOTO CAPTION
President Hosni Mubarak