According to the latest figures, Rajapaksa, a former Defence Minister, was leading in 17 districts (Kandy, Ratnapura, Anuradhapura, Polonnaruwa, Nuwaraeliya, Gampaha, Hambantota, Galle, Badulla, Kegale, Matara, Kurunegala, Puttalam, Kalutara, Colombo, Matale and Monaragala), whereas Premadasa was ahead in only five districts (Trincomalee, Jaffna, Batticaloa, Vanni, Digamadulla), reports Daily Mirror.
Sri Lanka has a total of 25 districts, organised into nine provinces.
Around 80 per cent of the nearly 16 million eligible Sri Lankans voted on Saturday to elect the country's eighth President.
In the Tamil-majority Northern Province, the polling percentage was recorded around 70 per cent with 66 per cent voter turnout in Jaffna district.
Former war-affected districts Kilinochchi polled 73 per cent, Mullaitivu 76 per cent, Vavuniya 75 and Mannar 71 per cent.
The percentage was a little less than the 2015 Presidential election when average voting percentage was 81.52 per cent out of which incumbent President Maithripala Sirisena won with 51.28 per cent with 6,217,162 votes while Mahinda Rajapaksa garnered 47.58 per cent with 5,768,090 votes.
Sirisena won in 12 districts while Rajapaksa won 10 districts.
The final results were expected by Sunday 6 p.m.
A record 35 candidates contested for the Presidency, but the main fight was confined between Rajapaksa and Premadasa.
Gotabaya is retired soldier who took over Sri Lanka's defence portfolio during the period when his older brother, Mahinda Rajapaksa was President (2005-2015) and also when Sri Lanka ended its war in 2009 with the Liberation Tigers of Tamil Eelam (LTTE).
He himself as a nationalist and a champion of the Sinhalese Buddhist majority and had also vowed to ensure strong national security in the wake of the April 21 Easter Sunday suicide bombings that killed over 250 people.
On the other hand, Sajith Premadasa, the son of Ranasinghe Premadasa who served as the President from 1989 until he was assassinated in May 1993 by the LTTE, has pledged to fight for the Muslim and Tamil minorities.
The votes from the minority community had also played a major role in Sirisena's 2015 victory.
( With inputs from IANS )