"These are extraordinary figures," said Zerhouni, whose ministry is scheduled to announce the final results on Friday.
Traditional opposition groups had warned the vote would be rigged and called on voters to stay away.
Al-Qaeda in Islamic Maghreb, a local offshoot of al-Qaeda, has also called for a boycott.
Outbreaks of violence
As voting progressed, sporadic riots were reported by the Associated Press and a bomb blast at a polling station in a province east of the capital injured two police officers.
Algeria suffered a protracted civil war in the 1990s, in which at least 150,000 people died after elections won by an Islamist party were annulled.
Incidents of violence have continued since and, should he win a third term, Bouteflika will still face the challenge of putting an end to the lingering insurgency.
Most Islamist leaders have been banned from politics.
In his campaigning, Bouteflika said: "I continue to regard the restoration of civil peace as a national priority, as long as hotbeds of tension and pockets of subversion survive."
Bouteflika faced five opponents in the election, including Louisa Hanoune, the leader of the Trotskyist Workers' Party and the only female candidate.
But analysts say the president, who has the full support of the government as well as labour and business unions, is almost certain to win.
He called for the constitution to be changed last year so he could run for a third term as president, and Algerian legislators acquiesced, clearing the way for him to stand again by abolishing term limits.
To date, Algeria has invested in roads, dams, and housing, as part of a $200bn programme funded through the country's oil and natural gas exports. But other sectors have declined due to under-investment.
Bouteflika is promising a $150bn development plan to create three million jobs and build one million homes over the next five years.
He has also hinted that he could offer an amnesty to al-Qaeda fighters if they renounce their campaign and turn themselves in.