Netumbo Nandi-Ndaitwah, from the governing South West Africa People's Organisation, is set to become Namibia's first female president with more than 90% of the votes from last week's disputed election now counted.
The electoral commission said she had won more than 58%, with her closest rival Itula, getting just over 25% of the vote share.
But following logistical problems and a three-day extension to polling in some parts of the country, Itula said on Saturday that his party would not recognise the results alleging electoral malpractice.
The governing party has been in power in the large but sparsely populated southern African country since independence in 1990.
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